Attachment 187281 Details for Bug 223094 – svn diff for biology/bcftools

[patch] svn diff for biology/bcftools

bcftools-1.6.diff (text/plain), 11.61 KB, created by Motomichi Matsuzaki on 2017-10-18 14:05:16 UTC

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Creator: Motomichi Matsuzaki

Created: 2017-10-18 14:05:16 UTC

Size: 11.61 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 452329)
>+++ Makefile	(working copy)
>@@ -2,8 +2,7 @@
> # $FreeBSD$
> 
> PORTNAME=	bcftools
>-PORTVERSION=	1.3.1
>-PORTREVISION=	2
>+PORTVERSION=	1.6
> CATEGORIES=	biology
> 
> MAINTAINER=	cartwright@asu.edu
>@@ -12,7 +11,7 @@
> LICENSE=	MIT
> # LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>-BUILD_DEPENDS=	htslib>=1.3:biology/htslib
>+BUILD_DEPENDS=	htslib>=1.6:biology/htslib
> LIB_DEPENDS=	libhts.so:biology/htslib
> TEST_DEPENDS=	bash:shells/bash
> 
>@@ -21,10 +20,12 @@
> USE_GITHUB=	yes
> GH_ACCOUNT=	samtools
> 
>-USES=		gmake perl5 shebangfix
>+USES=		autoreconf gmake perl5 python shebangfix
> USE_PERL5=	test
>+PYTHON_NO_DEPENDS=	yes
>+GNU_CONFIGURE=	yes
> SUB_FILES=	pkg-message
>-SHEBANG_FILES=	vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
>+SHEBANG_FILES=	misc/* test/test.pl
> 
> OPTIONS_DEFINE=	GPL
> GPL_DESC=	Enable modules that rely on GPL code
>@@ -37,19 +38,15 @@
> CPPFLAGS+=	-I${LOCALBASE}/include
> LDFLAGS+=	-L${LOCALBASE}/lib
> 
>-MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
>-		INSTALL_DATA="${INSTALL_DATA}" \
>-		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
>-		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
>-		INSTALL_DIR="${MKDIR}"
>-
> .if ${PORT_OPTIONS:MGPL}
> MAKE_ENV+=	USE_GPL=1
> LICENSE=	GPLv3
> .endif
> 
>-PLIST_SUB=	PORTVERSION="${PORTVERSION}"
>-
> TEST_TARGET=	test
> 
>+post-patch:
>+	@${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1)
>+	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
>+
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 452329)
>+++ distinfo	(working copy)
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1463692643
>-SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e
>-SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207
>+TIMESTAMP = 1508307708
>+SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025
>+SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 452329)
>+++ files/patch-Makefile	(working copy)
>@@ -1,19 +1,9 @@
>---- Makefile.orig	2015-12-15 21:42:34 UTC
>+--- Makefile.orig	2017-09-28 11:22:48 UTC
> +++ Makefile
>-@@ -29,16 +29,15 @@ TEST_PROG=  test/test-rbuf
>- all: $(PROG) $(TEST_PROG)
>+@@ -22,10 +22,10 @@
>+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
>+ # DEALINGS IN THE SOFTWARE.
>  
>- # Adjust $(HTSDIR) to point to your top-level htslib directory
>--HTSDIR = ../htslib
>--include $(HTSDIR)/htslib.mk
>--HTSLIB = $(HTSDIR)/libhts.a
>--BGZIP  = $(HTSDIR)/bgzip
>--TABIX  = $(HTSDIR)/tabix
>-+HTSDIR = $(prefix)/include
>-+HTSLIB = -lhts
>-+BGZIP  = $(HTSDIR)/../bin/bgzip
>-+TABIX  = $(HTSDIR)/../bin/tabix
>- 
> -CC       = gcc
> -CPPFLAGS =
> -CFLAGS   = -g -Wall -Wc++-compat -O2
>@@ -24,17 +14,13 @@
> +LDFLAGS  +=
>  LIBS     =
>  
>- OBJS     = main.o vcfindex.o tabix.o \
>-@@ -57,26 +56,20 @@ GSL_LIBS       =
>- ifdef USE_GPL
>-     EXTRA_CPPFLAGS += -DUSE_GPL
>-     OBJS += polysomy.o peakfit.o
>--    GSL_LIBS = -lgsl -lcblas
>-+    GSL_LIBS = -lgsl -lgslcblas
>- endif
>+ DYNAMIC_FLAGS = -rdynamic
>+@@ -42,26 +42,25 @@ OBJS     = main.o vcfindex.o tabix.o \
>+            vcfsort.o \
>+            ccall.o em.o prob1.o kmin.o # the original samtools calling
>  
> -prefix      = /usr/local
>-+prefix      = ${STAGEDIR}${PREFIX}
>++prefix      = ${PREFIX}
>  exec_prefix = $(prefix)
>  bindir      = $(exec_prefix)/bin
>  libdir      = $(exec_prefix)/lib
>@@ -42,37 +28,52 @@
> -mandir      = $(prefix)/share/man
> +mandir      = $(prefix)/man
>  man1dir     = $(mandir)/man1
>- 
>+ # Installation location for $(PLUGINS)
>  plugindir   = $(libexecdir)/bcftools
>  pluginpath  = $(plugindir)
>+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
>+-misc_bindir = $(bindir)
>++misc_bindir = $(bindir)/samtools_misc
>  
>--MKDIR_P = mkdir -p
>+ MKDIR_P = mkdir -p
> -INSTALL = install -p
>--INSTALL_PROGRAM = $(INSTALL)
> -INSTALL_DATA    = $(INSTALL) -m 644
> -INSTALL_DIR     = $(MKDIR_P) -m 755
>--
>- MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
>+-INSTALL_MAN     = $(INSTALL_DATA)
>+-INSTALL_PROGRAM = $(INSTALL)
>+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
>++INSTALL_DATA    = ${BSD_INSTALL_DATA}
>++INSTALL_DIR     = $(MKDIR_P)
>++INSTALL_MAN     = ${BSD_INSTALL_MAN}
>++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
>++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
>  
>- all:$(PROG) plugins
>-@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
>- 	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
>+ PROGRAMS = bcftools
>+ MISC_SCRIPTS = \
>+@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
>  
>- bcftools: $(HTSLIB) $(OBJS)
>--	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
>-+	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
>+ ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
>+ ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
>+-ALL_LIBS     = -lz -ldl $(LIBS)
>++ALL_LIBS     = -lz $(LIBS)
>  
>- doc/bcftools.1: doc/bcftools.txt
>- 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
>-@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
>+ # Usually config.mk and config.h are generated by running configure
>+ # or config.status, but if those aren't used create defaults here.
>+@@ -131,7 +130,7 @@ print-version:
>+ ifdef USE_GPL
>+     main.o : EXTRA_CPPFLAGS += -DUSE_GPL
>+     OBJS += polysomy.o peakfit.o
>+-    GSL_LIBS ?= -lgsl -lcblas
>++    GSL_LIBS ?= -lgsl -lgslcblas
>+ endif
>+ 
>+ bcftools: $(OBJS) $(HTSLIB)
>+@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
>  # Since there is no make dependency, bcftools.1 can be out-of-date and
>  # make docs can be run to update if asciidoc is available
>- install: $(PROG)
>+ install: $(PROG) $(PLUGINS)
> -	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
>--	$(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
>-+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
>-+	$(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
>-+	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
>- 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
>- 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
>- 
>++	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
>+ 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
>+ 	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
>+ 	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
>Index: files/patch-configure.ac
>===================================================================
>--- files/patch-configure.ac	(revision 0)
>+++ files/patch-configure.ac	(working copy)
>@@ -0,0 +1,11 @@
>+--- configure.ac.orig	2017-09-28 11:22:48 UTC
>++++ configure.ac
>+@@ -23,7 +23,7 @@
>+ # DEALINGS IN THE SOFTWARE.
>+ 
>+ dnl Process this file with autoconf to produce a configure script
>+-AC_INIT([BCFtools], m4_esyscmd_s([make print-version]),
>++AC_INIT([BCFtools], [@PORTVERSION@],
>+         [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
>+ AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
>+ AC_CONFIG_SRCDIR([main.c])
>
>Property changes on: files/patch-configure.ac
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-misc_run-roh.pl
>===================================================================
>--- files/patch-misc_run-roh.pl	(revision 0)
>+++ files/patch-misc_run-roh.pl	(working copy)
>@@ -0,0 +1,11 @@
>+--- misc/run-roh.pl.orig	2017-10-18 09:33:24 UTC
>++++ misc/run-roh.pl
>+@@ -97,7 +97,7 @@ sub cmd
>+     else 
>+     {      
>+         # child
>+-        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
>++        exec('/bin/sh', '-c', $cmd) or error("Failed to run the command [/bin/sh -c $cmd]: $!");
>+     }
>+ 
>+     if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }
>
>Property changes on: files/patch-misc_run-roh.pl
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-prob1.c
>===================================================================
>--- files/patch-prob1.c	(revision 452329)
>+++ files/patch-prob1.c	(working copy)
>@@ -1,4 +1,4 @@
>---- prob1.c.orig	2015-12-15 21:42:34 UTC
>+--- prob1.c.orig	2017-09-28 11:22:48 UTC
> +++ prob1.c
> @@ -33,6 +33,12 @@ THE SOFTWARE.  */
>  #include <zlib.h>
>Index: files/patch-test_test.pl
>===================================================================
>--- files/patch-test_test.pl	(revision 452329)
>+++ files/patch-test_test.pl	(working copy)
>@@ -1,6 +1,6 @@
>---- test/test.pl.orig	2015-12-22 22:45:13 UTC
>+--- test/test.pl.orig	2017-10-18 09:33:24 UTC
> +++ test/test.pl
>-@@ -290,7 +290,7 @@ sub _cmd
>+@@ -381,7 +381,7 @@ sub _cmd
>      else
>      {
>          # child
>@@ -9,7 +9,7 @@
>      }
>      return ($? >> 8, join('',@out));
>  }
>-@@ -657,7 +657,7 @@ sub test_usage
>+@@ -782,7 +782,7 @@ sub test_usage
>      my $command = $args{cmd};
>      my $commandpath = $$opts{bin}."/".$command;
>      my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
>@@ -18,7 +18,7 @@
>  
>      my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
>  
>-@@ -708,7 +708,7 @@ sub test_usage_subcommand
>+@@ -833,7 +833,7 @@ sub test_usage_subcommand
>      my $subcommand = $args{subcmd};
>      my $commandpath = $$opts{bin}."/".$command;
>      my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
>Index: files/pkg-message.in
>===================================================================
>--- files/pkg-message.in	(revision 452329)
>+++ files/pkg-message.in	(working copy)
>@@ -3,5 +3,5 @@
> 
> Add that directory to your path if you want to use these tools.
> 
>-Some of these tools depend on Perl5, and it will need to be installed to
>+Some of these tools depend on Perl5/Python, and it will need to be installed to
> use them.
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 452329)
>+++ pkg-plist	(working copy)
>@@ -1,19 +1,32 @@
> bin/bcftools
> bin/samtools_misc/color-chrs.pl
>+bin/samtools_misc/guess-ploidy.py
>+bin/samtools_misc/plot-roh.py
> bin/samtools_misc/plot-vcfstats
>+bin/samtools_misc/run-roh.pl
> bin/samtools_misc/vcfutils.pl
> libexec/bcftools/GTisec.so
>+libexec/bcftools/GTsubset.so
>+libexec/bcftools/ad-bias.so
>+libexec/bcftools/af-dist.so
>+libexec/bcftools/check-ploidy.so
>+libexec/bcftools/check-sparsity.so
> libexec/bcftools/color-chrs.so
> libexec/bcftools/counts.so
> libexec/bcftools/dosage.so
> libexec/bcftools/fill-AN-AC.so
>+libexec/bcftools/fill-from-fasta.so
> libexec/bcftools/fill-tags.so
> libexec/bcftools/fixploidy.so
>+libexec/bcftools/fixref.so
> libexec/bcftools/frameshifts.so
>+libexec/bcftools/guess-ploidy.so
> libexec/bcftools/impute-info.so
>+libexec/bcftools/isecGT.so
> libexec/bcftools/mendelian.so
> libexec/bcftools/missing2ref.so
>+libexec/bcftools/prune.so
> libexec/bcftools/setGT.so
> libexec/bcftools/tag2tag.so
>-libexec/bcftools/vcf2sex.so
>+libexec/bcftools/trio-switch-rate.so
> man/man1/bcftools.1.gz

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Attachments on bug 223094: 187279 | 187280 | 187281