Attachment 166591 Details for Bug 206939 – Poudriere log

Poudriere log

bowtie-1.1.2.log-10-1-amd64 (text/plain), 328.73 KB, created by Jason W. Bacon on 2016-02-05 03:53:44 UTC

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Creator: Jason W. Bacon

Created: 2016-02-05 03:53:44 UTC

Size: 328.73 KB

patch

obsolete

>build started at Thu Feb  4 21:46:28 CST 2016
>port directory: /usr/ports/biology/bowtie
>building for: FreeBSD 10-1-amd64-default 10.1-RELEASE-p29 FreeBSD 10.1-RELEASE-p29 amd64
>maintained by: bacon4000@gmail.com
>ident warning: no id keywords in /usr/local/poudriere/data/.m/10-1-amd64-default/ref//usr/ports/biology/bowtie/Makefile
>Makefile ident: 
>Poudriere version: 3.1.10
>Host OSVERSION: 1001000
>Jail OSVERSION: 1001000
>
>---Begin Environment---
>PKGREPOSITORY=/tmp/pkgs
>PACKAGES=/tmp/pkgs
>OSVERSION=1001000
>UNAME_v=FreeBSD 10.1-RELEASE-p29
>UNAME_r=10.1-RELEASE-p29
>BLOCKSIZE=K
>MAIL=/var/mail/root
>STATUS=1
>WARNING_WAIT=0
>SAVED_TERM=xterm
>NO_WARNING_PKG_INSTALL_EOL=yes
>MASTERMNT=/usr/local/poudriere/data/.m/10-1-amd64-default/ref
>FORCE_PACKAGE=yes
>PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
>POUDRIERE_BUILD_TYPE=bulk
>OLDPWD=/usr/wip/biology/bowtie
>PWD=/
>MASTERNAME=10-1-amd64-default
>SCRIPTPREFIX=/usr/local/share/poudriere
>USER=root
>HOME=/root
>POUDRIERE_VERSION=3.1.10
>SCRIPTPATH=/usr/local/share/poudriere/testport.sh
>TRYBROKEN=yes
>LIBEXECPREFIX=/usr/local/libexec/poudriere
>LOCALBASE=/usr/local
>PACKAGE_BUILDING=yes
>DEV_WARNING_WAIT=0
>---End Environment---
>
>---Begin OPTIONS List---
>---End OPTIONS List---
>
>--CONFIGURE_ARGS--
>
>--End CONFIGURE_ARGS--
>
>--CONFIGURE_ENV--
>MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work  HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
>--End CONFIGURE_ENV--
>
>--MAKE_ENV--
>XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work  HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" DONTSTRIP=yes NO_PIE=yes NO_DEBUG_FILES=yes SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="gcc48" CFLAGS="-pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing"  CPP="cpp48" CPPFLAGS=""  LDFLAGS=" -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS=""  CXX="g++48" CXXFLAGS="-pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48"  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install   -m 555"  BSD_INSTALL_LIB="install   -m 444"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
>--End MAKE_ENV--
>
>--PLIST_SUB--
>OSREL=10.1
>PREFIX=%D
>LOCALBASE=/usr/local
>RESETPREFIX=/usr/local
>PORTDOCS=""
>PORTEXAMPLES=""
>LIB32DIR=lib
>PERL_VERSION=5.20.3
>PERL_VER=5.20
>PERL5_MAN1=lib/perl5/site_perl/man/man1
>PERL5_MAN3=lib/perl5/site_perl/man/man3
>SITE_PERL=lib/perl5/site_perl
>SITE_ARCH=lib/perl5/site_perl/mach/5.20
>DOCSDIR="share/doc/bowtie"
>EXAMPLESDIR="share/examples/bowtie"
>DATADIR="share/bowtie"
>WWWDIR="www/bowtie"
>ETCDIR="etc/bowtie"
>--End PLIST_SUB--
>
>--SUB_LIST--
>PREFIX=/usr/local
>LOCALBASE=/usr/local
>DATADIR=/usr/local/share/bowtie
>DOCSDIR=/usr/local/share/doc/bowtie
>EXAMPLESDIR=/usr/local/share/examples/bowtie
>WWWDIR=/usr/local/www/bowtie
>ETCDIR=/usr/local/etc/bowtie
>--End SUB_LIST--
>
>---Begin make.conf---
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>PORTSDIR=/usr/ports
>PACKAGES=/packages
>DISTDIR=/distfiles
>---End make.conf---
>=======================<phase: check-sanity   >============================
>===>  License ART10 accepted by the user
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - not found
>===>   Installing existing package /packages/All/pkg-1.6.3.txz
>[10-1-amd64-default] Installing pkg-1.6.3...
>[10-1-amd64-default] Extracting pkg-1.6.3: .......... done
>Message from pkg-1.6.3:
>If you are upgrading from the old package format, first run:
>
>  # pkg2ng
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===>   Returning to build of bowtie-1.1.2
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License ART10 accepted by the user
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bowtie-1.1.2 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License ART10 accepted by the user
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bowtie-1.1.2 for building
>=> SHA256 Checksum OK for BenLangmead-bowtie-1.1.2-v1.1.2_GH0.tar.gz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License ART10 accepted by the user
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bowtie-1.1.2 for building
>===>  Extracting for bowtie-1.1.2
>=> SHA256 Checksum OK for BenLangmead-bowtie-1.1.2-v1.1.2_GH0.tar.gz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for bowtie-1.1.2
>===>  Applying FreeBSD patches for bowtie-1.1.2
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   bowtie-1.1.2 depends on executable: gmake - not found
>===>   Installing existing package /packages/All/gmake-4.1_2.txz
>[10-1-amd64-default] Installing gmake-4.1_2...
>[10-1-amd64-default] `-- Installing indexinfo-0.2.4...
>[10-1-amd64-default] `-- Extracting indexinfo-0.2.4: .... done
>[10-1-amd64-default] `-- Installing gettext-runtime-0.19.6...
>[10-1-amd64-default] `-- Extracting gettext-runtime-0.19.6: .......... done
>[10-1-amd64-default] Extracting gmake-4.1_2: .......... done
>===>   bowtie-1.1.2 depends on executable: gmake - found
>===>   Returning to build of bowtie-1.1.2
>===>   bowtie-1.1.2 depends on executable: gcc48 - not found
>===>   Installing existing package /packages/All/gcc-4.8.5_2.txz
>[10-1-amd64-default] Installing gcc-4.8.5_2...
>[10-1-amd64-default] `-- Installing mpc-1.0.3...
>[10-1-amd64-default] |   `-- Installing gmp-5.1.3_2...
>[10-1-amd64-default] |   `-- Extracting gmp-5.1.3_2: .......... done
>[10-1-amd64-default] |   `-- Installing mpfr-3.1.3...
>[10-1-amd64-default] |   `-- Extracting mpfr-3.1.3: .......... done
>[10-1-amd64-default] `-- Extracting mpc-1.0.3: ...... done
>[10-1-amd64-default] `-- Installing binutils-2.25.1,1...
>[10-1-amd64-default] `-- Extracting binutils-2.25.1,1: .......... done
>[10-1-amd64-default] `-- Installing gcc-ecj-4.5...
>[10-1-amd64-default] `-- Extracting gcc-ecj-4.5: . done
>[10-1-amd64-default] Extracting gcc-4.8.5_2: .......... done
>Message from gcc-4.8.5_2:
>To ensure binaries built with this toolchain find appropriate versions
>of the necessary run-time libraries, you may want to link using
>
>  -Wl,-rpath=/usr/local/lib/gcc48
>
>For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
>transparently.
>===>   bowtie-1.1.2 depends on executable: gcc48 - found
>===>   Returning to build of bowtie-1.1.2
>===>   bowtie-1.1.2 depends on file: /usr/local/bin/as - found
>===========================================================================
>=======================<phase: lib-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   bowtie-1.1.2 depends on executable: gmake - found
>===>   bowtie-1.1.2 depends on executable: gcc48 - found
>===>   bowtie-1.1.2 depends on file: /usr/local/bin/as - found
>===>  Configuring for bowtie-1.1.2
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for bowtie-1.1.2
>gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2'
>g++48 -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48 \""  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48   \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-build-s ebwt_build.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
>	-lpthread 
>g++48 -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48 \""  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48   \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-build-l ebwt_build.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
>	-lpthread 
>g++48 -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48 \""  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-align-s ebwt_search.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
>	-lpthread 
>g++48 -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48 \""  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-align-l ebwt_search.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
>	-lpthread 
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/find.h:62:0,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
>  typedef unsigned int TWord;
>                       ^
>In file included from SeqAn-1.1/seqan/find.h:62:0,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
>  typedef unsigned int TWord;
>                       ^
>In file included from SeqAn-1.1/seqan/index.h:82:0,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                 ^
>SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>In file included from SeqAn-1.1/seqan/index.h:82:0,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                 ^
>SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>In file included from SeqAn-1.1/seqan/index.h:83:0,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
>SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>In file included from SeqAn-1.1/seqan/index.h:83:0,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
>SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ebwt_search.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ebwt_search.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ebwt_search.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ebwt_search.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from ebwt_build.cpp:7:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from ebwt_build.cpp:7:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from ebwt_build.cpp:7:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from ebwt_build.cpp:7:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/index.h:82:0,
>                 from ebwt.h:16,
>                 from ebwt_search.cpp:14:
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                              ^
>In file included from SeqAn-1.1/seqan/index.h:82:0,
>                 from ebwt.h:16,
>                 from ebwt_search.cpp:14:
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                 ^
>SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                 ^
>SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>In file included from SeqAn-1.1/seqan/index.h:83:0,
>                 from ebwt.h:16,
>                 from ebwt_search.cpp:14:
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
>SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                              ^
>In file included from SeqAn-1.1/seqan/index.h:83:0,
>                 from ebwt.h:16,
>                 from ebwt_search.cpp:14:
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
>SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>In file included from ebwt.h:27:0,
>                 from ebwt_build.cpp:11:
>blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
>blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_build.cpp:11:
>blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
>blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_build.cpp:11:
>blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
>blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_build.cpp:11:
>blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
>blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_search.cpp:14:
>blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
>blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_search.cpp:14:
>blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
>blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_search.cpp:14:
>blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
>blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from ebwt_search.cpp:14:
>blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
>blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:40:0,
>                 from ebwt_build.cpp:11:
>reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
>reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
>    uint64_t origBufOff = bufOff;
>             ^
>reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
>          bool binarySearched = false;
>               ^
>In file included from ebwt.h:40:0,
>                 from ebwt_build.cpp:11:
>reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
>reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
>    uint64_t origBufOff = bufOff;
>             ^
>reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
>          bool binarySearched = false;
>               ^
>In file included from ebwt.h:40:0,
>                 from ebwt_search.cpp:14:
>reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
>reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
>    uint64_t origBufOff = bufOff;
>             ^
>reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
>          bool binarySearched = false;
>               ^
>In file included from ebwt.h:40:0,
>                 from ebwt_search.cpp:14:
>reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
>reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
>    uint64_t origBufOff = bufOff;
>             ^
>reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
>          bool binarySearched = false;
>               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_packed.h:1237:22:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostIn file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/index.h:27,
>                 from ebwt_build.cpp:5:
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_packed.h:1237:22:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
>SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>blockwise_sa.h:354:46:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VAspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
>SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>blockwise_sa.h:354:46:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
>                                     ^
>LUE / BITS_PER_VALUE),
>                                     ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:731:88:   required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>ebwt.h:4032:32:   required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = unsigned int; uint32_t = unsigned int]'
>ebwt_build.cpp:485:9:   required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]'
>ebwt_build.cpp:622:69:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:731:88:   required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>ebwt.h:4032:32:   required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = long unsigned int; uint32_t = unsigned int]'
>ebwt_build.cpp:485:9:   required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]'
>ebwt_build.cpp:622:69:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_packed.h:1237:22:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
>SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>blockwise_sa.h:354:46:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from ebwt_search.cpp:8:
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_packed.h:1237:22:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
>SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>blockwise_sa.h:354:46:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>g++48 -O \
>	-DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48 \""  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party -I . \
>	-o bowtie-inspect-s bowtie_inspect.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
>	-lpthread
>g++48 -O \
>	-DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48 \""  -DPOPCNT_CAPABILITY -pipe  -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -pipe -g -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party -I . \
>	-o bowtie-inspect-l bowtie_inspect.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
>	-lpthread
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/find.h:62:0,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
>  typedef unsigned int TWord;
>                       ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/find.h:62:0,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
>SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
>  typedef unsigned int TWord;
>                       ^
>In file included from SeqAn-1.1/seqan/index.h:82:0,
>                 from ebwt.h:16,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                 ^
>SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>In file included from SeqAn-1.1/seqan/index.h:83:0,
>                 from ebwt.h:16,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
>SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>In file included from SeqAn-1.1/seqan/index.h:82:0,
>                 from ebwt.h:16,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
>SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                 ^
>SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                        ^
>In file included from SeqAn-1.1/seqan/index.h:83:0,
>                 from ebwt.h:16,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
>SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                              ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
>SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
>                                                                           ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ebwt.h:24,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ebwt.h:24,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ebwt.h:24,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ebwt.h:24,
>                 from bowtie_inspect.cpp:10:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from bowtie_inspect.cpp:10:
>blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
>blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from bowtie_inspect.cpp:10:
>blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
>blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from bowtie_inspect.cpp:10:
>blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
>blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from ebwt.h:27:0,
>                 from bowtie_inspect.cpp:10:
>blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
>blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TStr>::Type TAlphabet;
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_packed.h:1237:22:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
>SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>blockwise_sa.h:354:46:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from SeqAn-1.1/seqan/find.h:31,
>                 from bowtie_inspect.cpp:6:
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_packed.h:1237:22:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
>SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>blockwise_sa.h:354:46:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
>                                     ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:509:6:   required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_base.h:1429:52:   required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_base.h:1459:67:   required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>ebwt.h:2965:35:   required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
>bowtie_inspect.cpp:283:2:   required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]'
>bowtie_inspect.cpp:461:42:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
>SeqAn-1.1/seqan/sequence/string_packed.h:509:6:   required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_base.h:1429:52:   required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]'
>SeqAn-1.1/seqan/sequence/string_base.h:1459:67:   required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]'
>ebwt.h:2965:35:   required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
>bowtie_inspect.cpp:283:2:   required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]'
>bowtie_inspect.cpp:461:42:   required from here
>SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from pat.cpp:6:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from pat.cpp:6:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from pat.cpp:5:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from pat.cpp:6:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from pat.cpp:6:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from ebwt_search_util.h:9,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from ebwt_search_util.h:9,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ebwt_search_util.h:8,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from ebwt_search_util.h:9,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from ebwt_search_util.h:9,
>                 from ebwt_search_util.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from ref_read.h:11,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from ref_read.h:12,
>                 from ref_read.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from hit_set.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from hit_set.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from hit_set.cpp:10:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from hit_set.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from hit_set.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from pat.h:13,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from pat.h:13,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from pat.h:12,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from pat.h:13,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from pat.h:13,
>                 from sam.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from alphabet.h:6,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from color_dec.cpp:11:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                 from SeqAn-1.1/seqan/sequence.h:27,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                           ^
>SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
>SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>                                                           ^
>In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
>SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Value<TLeft>::Type TLeftValue;
>                                      ^
>In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
>SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
>  typedef String<TTargetValue, TTargetSpec> TTarget;
>                                            ^
>In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
>SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Iterator<T, Standard>::Type TIterator;
>                                                ^
>SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
>SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
>                                                               ^
>In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                 from hit.h:11,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
>SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Id<TStringSet>::Type TId;
>                                         ^
>In file included from SeqAn-1.1/seqan/file.h:66:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
>SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Position<TAlign>::Type TPosition;
>                                          ^
>In file included from SeqAn-1.1/seqan/file.h:69:0,
>                 from alphabet.h:7,
>                 from hit.h:12,
>                 from hit.cpp:1:
>SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
>SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
>  typedef typename Row<TAlign>::Type TRow;
>                                     ^
>gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2'
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===>   bowtie-1.1.2 depends on executable: webbrowser - not found
>===>   Installing existing package /packages/All/webbrowser-0.3.txz
>[10-1-amd64-default] Installing webbrowser-0.3...
>[10-1-amd64-default] Extracting webbrowser-0.3: ..... done
>===>   bowtie-1.1.2 depends on executable: webbrowser - found
>===>   Returning to build of bowtie-1.1.2
>===>   bowtie-1.1.2 depends on executable: gcc48 - found
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - not found
>===>   Installing existing package /packages/All/perl5-5.20.3_8.txz
>[10-1-amd64-default] Installing perl5-5.20.3_8...
>[10-1-amd64-default] Extracting perl5-5.20.3_8: .......... done
>Message from perl5-5.20.3_8:
>The /usr/bin/perl symlink has been removed starting with Perl 5.20.
>For shebangs, you should either use:
>
>#!/usr/local/bin/perl
>
>or
>
>#!/usr/bin/env perl
>
>The first one will only work if you have a /usr/local/bin/perl,
>the second will work as long as perl is in PATH.
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found
>===>   Returning to build of bowtie-1.1.2
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for bowtie-1.1.2
>===>   bowtie-1.1.2 depends on executable: webbrowser - found
>===>   bowtie-1.1.2 depends on executable: gcc48 - found
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found
>===>   Generating temporary packing list
>install  -m 555  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie-build  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie-inspect  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin
>install   -m 555  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie*-s  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie*-l  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin
>install  -m 555  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/scripts/*.sh  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/scripts/*.pl  /usr/ports/biology/bowtie/files/bowtie-manual  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin
>/bin/mkdir -p /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie
>cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2 && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null  2>&1) &&  /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; &&  /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' --  'genomes indexes reads'  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie
>cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/doc && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null  2>&1) &&  /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; &&  /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' --  \*  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/doc/bowtie
>====> Compressing man pages (compress-man)
>===========================================================================
>====> Running Q/A tests (stage-qa)
>====> Checking for pkg-plist issues (check-plist)
>===> Parsing plist
>===> Checking for items in STAGEDIR missing from pkg-plist
>===> Checking for items in pkg-plist which are not in STAGEDIR
>===> No pkg-plist issues found (check-plist)
>====>> Checking for staging violations... done
>=======================<phase: package        >============================
>===>  Building package for bowtie-1.1.2
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for bowtie-1.1.2
>===>   bowtie-1.1.2 depends on executable: webbrowser - found
>===>   bowtie-1.1.2 depends on executable: gcc48 - found
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found
>===>  Checking if bowtie already installed
>===>   Registering installation for bowtie-1.1.2
>[10-1-amd64-default] Installing bowtie-1.1.2...
>===========================================================================
>====>> Checking shared library dependencies
> 0x0000000000000001 (NEEDED)             Shared library: [libc.so.7]
> 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for bowtie
>===>   Deinstalling bowtie-1.1.2
>Updating database digests format: .......... done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	bowtie-1.1.2
>
>The operation will free 32 MiB.
>[10-1-amd64-default] [1/1] Deinstalling bowtie-1.1.2...
>[10-1-amd64-default] [1/1] Deleting files for bowtie-1.1.2: .......... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:01:20] ====>> Installing from package
>[10-1-amd64-default] Installing bowtie-1.1.2...
>[10-1-amd64-default] Extracting bowtie-1.1.2: .......... done
>[00:01:21] ====>> Cleaning up
>===>  Cleaning for bowtie-1.1.2
>[00:01:21] ====>> Deinstalling package
>Updating database digests format: . done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	bowtie-1.1.2
>
>The operation will free 32 MiB.
>[10-1-amd64-default] [1/1] Deinstalling bowtie-1.1.2...
>[10-1-amd64-default] [1/1] Deleting files for bowtie-1.1.2: .......... done
>build of biology/bowtie ended at Thu Feb  4 21:47:46 CST 2016
>build time: 00:01:18

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Attachments on bug 206939: 166589 | 166590 | 166591 | 167715 | 167716 | 167717