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(-)biology/ngs-sdk/Makefile (+42 lines)
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# $FreeBSD$
2
3
PORTNAME=	ngs
4
PORTVERSION=	1.3.0
5
CATEGORIES=	biology
6
PKGNAMESUFFIX=	-sdk
7
8
MAINTAINER=	mzaki@niid.go.jp
9
COMMENT=	NCBI's front-end API for NGS data manipulation
10
11
LICENSE=	PD
12
LICENSE_FILE=	${WRKSRC}/../LICENSE
13
14
USE_GITHUB=	yes
15
GH_ACCOUNT=	ncbi
16
17
USES=		compiler gmake perl5
18
USE_PERL5=	build
19
GNU_CONFIGURE=	yes
20
CONFIGURE_ARGS=	CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
21
USE_LDCONFIG=	yes
22
23
WRKSRC_SUBDIR=	ngs-sdk
24
ALL_TARGET=	subtargs
25
26
# for port developpers, building with these options may fail
27
OPTIONS_DEFINE=	EXAMPLES GCC DEBUG OPTIMIZED_CFLAGS TEST
28
DEBUG_PREVENTS=	OPTIMIZED_CFLAGS
29
DEBUG_CONFIGURE_WITH=	debug
30
GCC_USE=	gcc=yes
31
OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
32
TEST_TEST_TARGET=	test
33
34
post-build-TEST-on:	do-test
35
36
do-install:
37
	@(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copylibs copyincludes)
38
39
post-install-EXAMPLES-on:
40
	@(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copyexamples)
41
42
.include <bsd.port.mk>
(-)biology/ngs-sdk/distinfo (+3 lines)
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TIMESTAMP = 1504850804
2
SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2
3
SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187
(-)biology/ngs-sdk/files/patch-Makefile.install (+22 lines)
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--- Makefile.install.orig	2016-10-07 21:59:36 UTC
2
+++ Makefile.install
3
@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \
4
     ngs-c++.$(VERSION_LIBX) \
5
     ngs-adapt-c++.$(VERSION_LIBX) \
6
 
7
-LIB_TARGET = $(INST_LIBDIR)$(BITS)
8
+LIB_TARGET = $(INST_LIBDIR)
9
 
10
 LIBRARIES_WITH_PREFIX = \
11
 	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
12
@@ -53,8 +53,8 @@ copyincludes:
13
 
14
 copyexamples:
15
 	@ echo "Installing examples to $(INST_SHAREDIR)"
16
-	@ mkdir -p $(INST_SHAREDIR)/examples
17
-	@ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples
18
+	@ mkdir -p $(INST_SHAREDIR)/examples/ngs
19
+	@ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples/ngs
20
 
21
 #fake root for debugging
22
 #uncomment this line and change the test for root ( see under install: ) to succeed:
(-)biology/ngs-sdk/files/patch-Makefile.libs (+11 lines)
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--- Makefile.libs.orig	2016-10-07 21:59:36 UTC
2
+++ Makefile.libs
3
@@ -109,7 +109,7 @@ SDK_DEPS =                             \
4
 	$(ILIBDIR)/$(LPFX)ngs-disp.$(LIBX)
5
 
6
 $(LIBDIR)/$(LPFX)ngs-sdk.$(VERSION_SHLX): $(SDK_DEPS)
7
-	$(LP) $(DBG) $(OPT) -shared -o $@ $(SONAME) `cat $(addsuffix /manifest,$(SDK_XLIBS))` $(SDK_LIB)
8
+	$(LP) $(DBG) $(OPT) -shared -o $@ $(LDFLAGS) $(SONAME) `cat $(addsuffix /manifest,$(SDK_XLIBS))` $(SDK_LIB)
9
 
10
 $(LIBDIR)/$(LPFX)ngs-sdk.$(MAJVERS_SHLX): $(LIBDIR)/$(LPFX)ngs-sdk.$(VERSION_SHLX)
11
 	rm -f $@
(-)biology/ngs-sdk/files/patch-setup_konfigure.perl (+228 lines)
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--- setup/konfigure.perl.orig	2016-10-07 21:59:36 UTC
2
+++ setup/konfigure.perl
3
@@ -186,7 +186,7 @@ if ($OPT{'help'}) {
4
 foreach (@ARGV) {
5
     @_ = split('=');
6
     next if ($#_ != 1);
7
-    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS');
8
+    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS');
9
 }
10
 
11
 println "Configuring $PACKAGE_NAME package";
12
@@ -198,7 +198,7 @@ print "checking system type... " unless 
13
 my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
14
 println $OSTYPE unless ($AUTORUN);
15
 
16
-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
17
+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
18
     println "configure: error: unsupported system '$OSTYPE'";
19
     exit 1;
20
 }
21
@@ -213,7 +213,7 @@ if ($OS eq 'linux') {
22
 
23
 print "checking machine architecture... " unless ($AUTORUN);
24
 println $MARCH unless ($AUTORUN);
25
-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
26
+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i) {
27
     println "configure: error: unsupported architecture '$OSTYPE'";
28
     exit 1;
29
 }
30
@@ -298,7 +298,7 @@ print "checking for supported architectu
31
 
32
 my $BITS;
33
 
34
-if ($MARCH =~ /x86_64/i) {
35
+if ($MARCH =~ /(x86_|amd)64/i) {
36
     $BITS = 64;
37
 } elsif ($MARCH eq 'fat86') {
38
     $BITS = '32_64';
39
@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) {
40
     $EXEX = '';
41
     $OSINC = 'unix';
42
     $TOOLS = 'clang' unless ($TOOLS);
43
+} elsif ($OSTYPE =~ /freebsd/i) {
44
+    $LPFX = 'lib';
45
+    $OBJX = 'o';
46
+    $LOBX = 'pic.o';
47
+    $LIBX = 'a';
48
+    $SHLX = 'so';
49
+    $EXEX = '';
50
+    $OSINC = 'unix';
51
+    unless ($TOOLS) {
52
+        $TOOLS = 'clang';
53
+        $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS});
54
+    }
55
 } elsif ($OSTYPE eq 'win') {
56
     $TOOLS = 'vc++';
57
 } else {
58
@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M
59
 
60
 print "checking for supported tool chain... " unless ($AUTORUN);
61
 
62
+$CC      = $OPT{CC     } if ($OPT{CC     });
63
 $CPP     = $OPT{CXX    } if ($OPT{CXX    });
64
 $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS});
65
 
66
 if ($TOOLS =~ /gcc$/) {
67
     $CPP  = 'g++' unless ($CPP);
68
-    $CC   = "$TOOLS -c";
69
+    $CC   = 'gcc' unless ($CC);
70
+    $LD   = $CC;
71
+    $CC   = "$CC -c";
72
     $CP   = "$CPP -c";
73
     $AR   = 'ar rc';
74
     $ARX  = 'ar x';
75
     $ARLS = 'ar t';
76
-    $LD   = $TOOLS;
77
     $LP   = $CPP;
78
 
79
     $DBG = '-g -DDEBUG';
80
@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) {
81
     $MD  = '-MD';
82
 } elsif ($TOOLS eq 'clang') {
83
     $CPP  = 'clang++' unless ($CPP);
84
-    $CC   = 'clang -c';
85
-    my $versionMin = '-mmacosx-version-min=10.6';
86
+    $CC   = 'clang' unless ($CC);
87
+    $LD   = $CC;
88
+    $CC   = "$CC -c";
89
+    my $versionMin = '';
90
+    $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i);
91
     $CP   = "$CPP -c $versionMin";
92
     if ($BITS ne '32_64') {
93
-        $ARCH_FL = '-arch i386' if ($BITS == 32);
94
+        $ARCH_FL = '-arch i386' if ($OSTYPE =~ /darwin/i && $BITS == 32);
95
         $OPT = '-O3';
96
         $AR      = 'ar rc';
97
-        $LD      = "clang $ARCH_FL";
98
+        $LD      = "$LD $ARCH_FL";
99
         $LP      = "$CPP $versionMin $ARCH_FL";
100
     } else {
101
         $MAKE_MANIFEST = '( echo "$^" > $@/manifest )';
102
         $ARCH_FL       = '-arch i386 -arch x86_64';
103
         $OPT    = '-O3';
104
         $AR     = 'libtool -static -o';
105
-        $LD     = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
106
+        $LD     = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
107
         $LP     = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
108
     }
109
     $ARX  = 'ar x';
110
@@ -755,13 +772,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os
111
 # install paths
112
 EndText
113
 
114
-    L($F, "INST_BINDIR = $OPT{'bindir'}"      ) if ($OPT{'bindir'});
115
-    L($F, "INST_LIBDIR = $OPT{'libdir'}"      ) if ($OPT{'libdir'});
116
-    L($F, "INST_INCDIR = $OPT{'includedir'}"  ) if ($OPT{'includedir'});
117
-    L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'});
118
-    L($F, "INST_SHAREDIR = $OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
119
-    L($F, "INST_JARDIR = $OPT{'javadir'}"     ) if ($OPT{'javadir'});
120
-    L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'});
121
+    L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}"      ) if ($OPT{'bindir'});
122
+    L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}"      ) if ($OPT{'libdir'});
123
+    L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}"  ) if ($OPT{'includedir'});
124
+    L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'});
125
+    L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
126
+    L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}"     ) if ($OPT{'javadir'});
127
+    L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'});
128
 
129
     my ($E_VERSION_SHLX, $VERSION_SHLX,
130
         $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX);
131
@@ -825,7 +842,7 @@ MAJMIN_EXEX  = \$(EXEX).\$(MAJMIN)
132
 MAJVERS_EXEX = \$(EXEX).\$(MAJVERS)
133
 
134
 # system architecture and wordsize
135
-ARCH = $ARCH
136
+override ARCH = $ARCH
137
 EndText
138
 
139
     L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH);
140
@@ -860,7 +877,7 @@ EndText
141
     }
142
     L($F, "PIC     = $PIC") if ($PIC);
143
     if ($PKG{LNG} eq 'C') {
144
-        if ($TOOLS =~ /clang/i) {
145
+        if ($OSTYPE =~ /darwin/i) {
146
    L($F, 'SONAME  = -install_name ' .
147
                '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
148
    L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
149
@@ -884,7 +901,7 @@ EndText
150
         }
151
     }
152
     if ($PKG{LNG} eq 'C') {
153
-        L($F, "CFLAGS  = \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL");
154
+        L($F, "CFLAGS  += \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL");
155
     }
156
     L($F, "LDFLAGS = $LDFLAGS") if ($LDFLAGS);
157
 
158
@@ -970,7 +987,7 @@ EndText
159
     L($F, '# directory rules');
160
     if ($PKG{LNG} eq 'C') {
161
         L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
162
-            . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
163
+            . '$(OBJDIR) $(INST_LIBDIR):');
164
         T($F, 'mkdir -p $@');
165
     } elsif ($PKG{LNG} eq 'JAVA') {
166
         # test if we have jni header path
167
@@ -1000,12 +1017,12 @@ EndText
168
     L($F, 'export CONFIGURE_FOUND_XML2');
169
     L($F);
170
 
171
-    if ($OS eq 'linux' || $OS eq 'mac') {
172
+    if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') {
173
         L($F, '# installation rules');
174
         L($F,
175
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
176
+        '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
177
         T($F, '@ echo -n "installing \'$(@F)\'... "');
178
-        T($F, '@ if cp $^ $@ && chmod 644 $@;                         \\');
179
+        T($F, '@ if $(BSD_INSTALL_DATA) $^ $@;                        \\');
180
         T($F, '  then                                                 \\');
181
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
182
                      . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) '
183
@@ -1014,7 +1031,7 @@ EndText
184
         T($F, '      ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
185
                       . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
186
         T($F, '      ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
187
-   '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
188
+   '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
189
                                                               . ' \\');
190
         T($F, '      echo success;                                    \\');
191
         T($F, '  else                                                 \\');
192
@@ -1024,15 +1041,15 @@ EndText
193
         L($F);
194
 
195
         L($F,
196
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
197
+        '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
198
         T($F, '@ echo -n "installing \'$(@F)\'... "');
199
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
200
+        T($F, '@ if $(BSD_INSTALL_LIB) $^ $@;                         \\');
201
         T($F, '  then                                                 \\');
202
         if ($OS ne 'mac') {
203
           T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
204
                       . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@);    \\');
205
         }
206
-        if ($OS eq 'linux') {
207
+        if ($OS eq 'linux' || $OS eq 'bsd') {
208
           T($F, '      ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\');
209
         } elsif ($OS eq 'mac') {
210
           T($F, '      ln -sf $(@F) '
211
@@ -1051,7 +1068,7 @@ EndText
212
 
213
         L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)');
214
         T($F, '@ echo -n "installing \'$(@F)\'... "');
215
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
216
+        T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@;                     \\');
217
         T($F, '  then                                                 \\');
218
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
219
                       . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@);     \\');
220
@@ -1333,7 +1350,7 @@ sub find_in_dir {
221
                 ++$found;
222
             }
223
             if (! $found) {
224
-                my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
225
+                my $libdir = File::Spec->catdir($dir, 'lib');
226
                 my $f = File::Spec->catdir($libdir, $lib);
227
                 print "\tchecking $f\n\t" if ($OPT{'debug'});
228
                 if (-e $f) {
(-)biology/ngs-sdk/files/patch-setup_os-arch.prl (+20 lines)
Line 0 Link Here
1
--- setup/os-arch.prl.orig	2016-10-07 21:59:36 UTC
2
+++ setup/os-arch.prl
3
@@ -11,6 +11,8 @@ sub OsArch {
4
         chomp $UNAME;
5
         if ($UNAME =~ /Darwin/) {
6
             $HOST_OS = 'mac';
7
+        } elsif ($UNAME =~ /.*BSD/) {
8
+            $HOST_OS = 'bsd';
9
         } elsif ($UNAME =~ /Linux/) {
10
             $HOST_OS = 'linux';
11
         } elsif ($UNAME =~ /SunOS/) {
12
@@ -49,6 +51,8 @@ sub OsArch {
13
                 }
14
             } elsif ($MARCH =~ /x86_64/) {
15
                 $HOST_ARCH = 'x86_64';
16
+            } elsif ($MARCH =~ /amd64/) {
17
+                $HOST_ARCH = 'x86_64';
18
             } elsif ($MARCH =~ /i86pc/) {
19
                 $HOST_ARCH = 'x86_64';
20
                 @ARCHITECTURES = qw(x86_64 i386);
(-)biology/ngs-sdk/pkg-descr (+14 lines)
Line 0 Link Here
1
NGS is NCBI's 'front-end' API for accessing reads, alignments and pileups
2
produced from Next Generation Sequencing. The 'back-end' engine are provided
3
by biology/ncbi-vdb port.
4
5
Although the GitHub repository contains C++, Java and Python libraries,
6
this port only install the following libraries to simplify dependencies.
7
8
libngs-c++.a       C++ front-end API
9
libngs-adapt-c++.a C++ adapter for C-based protocol to back-end engine
10
libngs-sdk.so      Java and Python language bindings of the front-end API
11
12
See ${WRKSRC}/CONTENTS for the detail.
13
14
WWW: https://github.com/ncbi/ngs/wiki
(-)biology/ngs-sdk/pkg-plist (+109 lines)
Line 0 Link Here
1
include/ngs/Alignment.hpp
2
include/ngs/AlignmentIterator.hpp
3
include/ngs/ErrorMsg.hpp
4
include/ngs/Fragment.hpp
5
include/ngs/FragmentIterator.hpp
6
include/ngs/Package.hpp
7
include/ngs/Pileup.hpp
8
include/ngs/PileupEvent.hpp
9
include/ngs/PileupEventIterator.hpp
10
include/ngs/PileupIterator.hpp
11
include/ngs/Read.hpp
12
include/ngs/ReadCollection.hpp
13
include/ngs/ReadGroup.hpp
14
include/ngs/ReadGroupIterator.hpp
15
include/ngs/ReadIterator.hpp
16
include/ngs/Reference.hpp
17
include/ngs/ReferenceIterator.hpp
18
include/ngs/ReferenceSequence.hpp
19
include/ngs/Statistics.hpp
20
include/ngs/StringRef.hpp
21
include/ngs/adapter/AlignmentItf.hpp
22
include/ngs/adapter/ErrorMsg.hpp
23
include/ngs/adapter/FragmentItf.hpp
24
include/ngs/adapter/PileupEventItf.hpp
25
include/ngs/adapter/PileupItf.hpp
26
include/ngs/adapter/ReadCollectionItf.hpp
27
include/ngs/adapter/ReadGroupItf.hpp
28
include/ngs/adapter/ReadItf.hpp
29
include/ngs/adapter/Refcount.hpp
30
include/ngs/adapter/ReferenceItf.hpp
31
include/ngs/adapter/ReferenceSequenceItf.hpp
32
include/ngs/adapter/StatisticsItf.hpp
33
include/ngs/adapter/StringItf.hpp
34
include/ngs/adapter/defs.h
35
include/ngs/inl/Alignment.hpp
36
include/ngs/inl/AlignmentIterator.hpp
37
include/ngs/inl/Fragment.hpp
38
include/ngs/inl/FragmentIterator.hpp
39
include/ngs/inl/Package.hpp
40
include/ngs/inl/Pileup.hpp
41
include/ngs/inl/PileupEvent.hpp
42
include/ngs/inl/PileupEventIterator.hpp
43
include/ngs/inl/PileupIterator.hpp
44
include/ngs/inl/Read.hpp
45
include/ngs/inl/ReadCollection.hpp
46
include/ngs/inl/ReadGroup.hpp
47
include/ngs/inl/ReadGroupIterator.hpp
48
include/ngs/inl/ReadIterator.hpp
49
include/ngs/inl/Reference.hpp
50
include/ngs/inl/ReferenceIterator.hpp
51
include/ngs/inl/ReferenceSequence.hpp
52
include/ngs/inl/Statistics.hpp
53
include/ngs/inl/StringRef.hpp
54
include/ngs/itf/AlignmentItf.h
55
include/ngs/itf/AlignmentItf.hpp
56
include/ngs/itf/ErrBlock.h
57
include/ngs/itf/ErrBlock.hpp
58
include/ngs/itf/ErrorMsg.hpp
59
include/ngs/itf/FragmentItf.h
60
include/ngs/itf/FragmentItf.hpp
61
include/ngs/itf/PackageItf.hpp
62
include/ngs/itf/PileupEventItf.h
63
include/ngs/itf/PileupEventItf.hpp
64
include/ngs/itf/PileupItf.h
65
include/ngs/itf/PileupItf.hpp
66
include/ngs/itf/ReadCollectionItf.h
67
include/ngs/itf/ReadCollectionItf.hpp
68
include/ngs/itf/ReadGroupItf.h
69
include/ngs/itf/ReadGroupItf.hpp
70
include/ngs/itf/ReadItf.h
71
include/ngs/itf/ReadItf.hpp
72
include/ngs/itf/Refcount.h
73
include/ngs/itf/Refcount.hpp
74
include/ngs/itf/ReferenceItf.h
75
include/ngs/itf/ReferenceItf.hpp
76
include/ngs/itf/ReferenceSequenceItf.h
77
include/ngs/itf/ReferenceSequenceItf.hpp
78
include/ngs/itf/StatisticsItf.h
79
include/ngs/itf/StatisticsItf.hpp
80
include/ngs/itf/StringItf.h
81
include/ngs/itf/StringItf.hpp
82
include/ngs/itf/VTable.h
83
include/ngs/itf/VTable.hpp
84
include/ngs/itf/defs.h
85
include/ngs/unix/fat86/atomic32.h
86
include/ngs/unix/i386/atomic32.h
87
include/ngs/unix/x86_64/atomic32.h
88
include/ngs/win/atomic32.h
89
include/ngs/win/stdbool.h
90
lib/libngs-adapt-c++-static.a
91
lib/libngs-adapt-c++.a
92
lib/libngs-adapt-c++.a.1
93
lib/libngs-adapt-c++.a.1.3.0
94
lib/libngs-c++-static.a
95
lib/libngs-c++.a
96
lib/libngs-c++.a.1
97
lib/libngs-c++.a.1.3.0
98
lib/libngs-sdk.so
99
lib/libngs-sdk.so.1
100
lib/libngs-sdk.so.1.3.0
101
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
102
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
103
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
104
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FastqTableDump.cpp
105
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp
106
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
107
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.config
108
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp
109
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp

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