Index: biology/ngs-sdk/Makefile =================================================================== --- biology/ngs-sdk/Makefile (nonexistent) +++ biology/ngs-sdk/Makefile (working copy) @@ -0,0 +1,42 @@ +# $FreeBSD$ + +PORTNAME= ngs +PORTVERSION= 1.3.0 +CATEGORIES= biology +PKGNAMESUFFIX= -sdk + +MAINTAINER= mzaki@niid.go.jp +COMMENT= NCBI's front-end API for NGS data manipulation + +LICENSE= PD +LICENSE_FILE= ${WRKSRC}/../LICENSE + +USE_GITHUB= yes +GH_ACCOUNT= ncbi + +USES= compiler gmake perl5 +USE_PERL5= build +GNU_CONFIGURE= yes +CONFIGURE_ARGS= CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" +USE_LDCONFIG= yes + +WRKSRC_SUBDIR= ngs-sdk +ALL_TARGET= subtargs + +# for port developpers, building with these options may fail +OPTIONS_DEFINE= EXAMPLES GCC DEBUG OPTIMIZED_CFLAGS TEST +DEBUG_PREVENTS= OPTIMIZED_CFLAGS +DEBUG_CONFIGURE_WITH= debug +GCC_USE= gcc=yes +OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT="" +TEST_TEST_TARGET= test + +post-build-TEST-on: do-test + +do-install: + @(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copylibs copyincludes) + +post-install-EXAMPLES-on: + @(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copyexamples) + +.include Property changes on: biology/ngs-sdk/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/ngs-sdk/distinfo =================================================================== --- biology/ngs-sdk/distinfo (nonexistent) +++ biology/ngs-sdk/distinfo (working copy) @@ -0,0 +1,3 @@ +TIMESTAMP = 1504850804 +SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2 +SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187 Property changes on: biology/ngs-sdk/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/ngs-sdk/files/patch-Makefile.install =================================================================== --- biology/ngs-sdk/files/patch-Makefile.install (nonexistent) +++ biology/ngs-sdk/files/patch-Makefile.install (working copy) @@ -0,0 +1,22 @@ +--- Makefile.install.orig 2016-10-07 21:59:36 UTC ++++ Makefile.install +@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \ + ngs-c++.$(VERSION_LIBX) \ + ngs-adapt-c++.$(VERSION_LIBX) \ + +-LIB_TARGET = $(INST_LIBDIR)$(BITS) ++LIB_TARGET = $(INST_LIBDIR) + + LIBRARIES_WITH_PREFIX = \ + $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL)) +@@ -53,8 +53,8 @@ copyincludes: + + copyexamples: + @ echo "Installing examples to $(INST_SHAREDIR)" +- @ mkdir -p $(INST_SHAREDIR)/examples +- @ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples ++ @ mkdir -p $(INST_SHAREDIR)/examples/ngs ++ @ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples/ngs + + #fake root for debugging + #uncomment this line and change the test for root ( see under install: ) to succeed: Property changes on: biology/ngs-sdk/files/patch-Makefile.install ___________________________________________________________________ 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: biology/ngs-sdk/files/patch-Makefile.libs =================================================================== --- biology/ngs-sdk/files/patch-Makefile.libs (nonexistent) +++ biology/ngs-sdk/files/patch-Makefile.libs (working copy) @@ -0,0 +1,11 @@ +--- Makefile.libs.orig 2016-10-07 21:59:36 UTC ++++ Makefile.libs +@@ -109,7 +109,7 @@ SDK_DEPS = \ + $(ILIBDIR)/$(LPFX)ngs-disp.$(LIBX) + + $(LIBDIR)/$(LPFX)ngs-sdk.$(VERSION_SHLX): $(SDK_DEPS) +- $(LP) $(DBG) $(OPT) -shared -o $@ $(SONAME) `cat $(addsuffix /manifest,$(SDK_XLIBS))` $(SDK_LIB) ++ $(LP) $(DBG) $(OPT) -shared -o $@ $(LDFLAGS) $(SONAME) `cat $(addsuffix /manifest,$(SDK_XLIBS))` $(SDK_LIB) + + $(LIBDIR)/$(LPFX)ngs-sdk.$(MAJVERS_SHLX): $(LIBDIR)/$(LPFX)ngs-sdk.$(VERSION_SHLX) + rm -f $@ Property changes on: biology/ngs-sdk/files/patch-Makefile.libs ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/ngs-sdk/files/patch-setup_konfigure.perl =================================================================== --- biology/ngs-sdk/files/patch-setup_konfigure.perl (nonexistent) +++ biology/ngs-sdk/files/patch-setup_konfigure.perl (working copy) @@ -0,0 +1,228 @@ +--- setup/konfigure.perl.orig 2016-10-07 21:59:36 UTC ++++ setup/konfigure.perl +@@ -186,7 +186,7 @@ if ($OPT{'help'}) { + foreach (@ARGV) { + @_ = split('='); + next if ($#_ != 1); +- $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS'); ++ $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS'); + } + + println "Configuring $PACKAGE_NAME package"; +@@ -198,7 +198,7 @@ print "checking system type... " unless + my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch(); + println $OSTYPE unless ($AUTORUN); + +-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { ++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { + println "configure: error: unsupported system '$OSTYPE'"; + exit 1; + } +@@ -213,7 +213,7 @@ if ($OS eq 'linux') { + + print "checking machine architecture... " unless ($AUTORUN); + println $MARCH unless ($AUTORUN); +-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) { ++unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i) { + println "configure: error: unsupported architecture '$OSTYPE'"; + exit 1; + } +@@ -298,7 +298,7 @@ print "checking for supported architectu + + my $BITS; + +-if ($MARCH =~ /x86_64/i) { ++if ($MARCH =~ /(x86_|amd)64/i) { + $BITS = 64; + } elsif ($MARCH eq 'fat86') { + $BITS = '32_64'; +@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) { + $EXEX = ''; + $OSINC = 'unix'; + $TOOLS = 'clang' unless ($TOOLS); ++} elsif ($OSTYPE =~ /freebsd/i) { ++ $LPFX = 'lib'; ++ $OBJX = 'o'; ++ $LOBX = 'pic.o'; ++ $LIBX = 'a'; ++ $SHLX = 'so'; ++ $EXEX = ''; ++ $OSINC = 'unix'; ++ unless ($TOOLS) { ++ $TOOLS = 'clang'; ++ $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS}); ++ } + } elsif ($OSTYPE eq 'win') { + $TOOLS = 'vc++'; + } else { +@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M + + print "checking for supported tool chain... " unless ($AUTORUN); + ++$CC = $OPT{CC } if ($OPT{CC }); + $CPP = $OPT{CXX } if ($OPT{CXX }); + $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS}); + + if ($TOOLS =~ /gcc$/) { + $CPP = 'g++' unless ($CPP); +- $CC = "$TOOLS -c"; ++ $CC = 'gcc' unless ($CC); ++ $LD = $CC; ++ $CC = "$CC -c"; + $CP = "$CPP -c"; + $AR = 'ar rc'; + $ARX = 'ar x'; + $ARLS = 'ar t'; +- $LD = $TOOLS; + $LP = $CPP; + + $DBG = '-g -DDEBUG'; +@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) { + $MD = '-MD'; + } elsif ($TOOLS eq 'clang') { + $CPP = 'clang++' unless ($CPP); +- $CC = 'clang -c'; +- my $versionMin = '-mmacosx-version-min=10.6'; ++ $CC = 'clang' unless ($CC); ++ $LD = $CC; ++ $CC = "$CC -c"; ++ my $versionMin = ''; ++ $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i); + $CP = "$CPP -c $versionMin"; + if ($BITS ne '32_64') { +- $ARCH_FL = '-arch i386' if ($BITS == 32); ++ $ARCH_FL = '-arch i386' if ($OSTYPE =~ /darwin/i && $BITS == 32); + $OPT = '-O3'; + $AR = 'ar rc'; +- $LD = "clang $ARCH_FL"; ++ $LD = "$LD $ARCH_FL"; + $LP = "$CPP $versionMin $ARCH_FL"; + } else { + $MAKE_MANIFEST = '( echo "$^" > $@/manifest )'; + $ARCH_FL = '-arch i386 -arch x86_64'; + $OPT = '-O3'; + $AR = 'libtool -static -o'; +- $LD = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; ++ $LD = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; + $LP = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; + } + $ARX = 'ar x'; +@@ -755,13 +772,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os + # install paths + EndText + +- L($F, "INST_BINDIR = $OPT{'bindir'}" ) if ($OPT{'bindir'}); +- L($F, "INST_LIBDIR = $OPT{'libdir'}" ) if ($OPT{'libdir'}); +- L($F, "INST_INCDIR = $OPT{'includedir'}" ) if ($OPT{'includedir'}); +- L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'}); +- L($F, "INST_SHAREDIR = $OPT{'sharedir'}" ) if ($OPT{'sharedir'}); +- L($F, "INST_JARDIR = $OPT{'javadir'}" ) if ($OPT{'javadir'}); +- L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'}); ++ L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}" ) if ($OPT{'bindir'}); ++ L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}" ) if ($OPT{'libdir'}); ++ L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}" ) if ($OPT{'includedir'}); ++ L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'}); ++ L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}" ) if ($OPT{'sharedir'}); ++ L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}" ) if ($OPT{'javadir'}); ++ L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'}); + + my ($E_VERSION_SHLX, $VERSION_SHLX, + $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX); +@@ -825,7 +842,7 @@ MAJMIN_EXEX = \$(EXEX).\$(MAJMIN) + MAJVERS_EXEX = \$(EXEX).\$(MAJVERS) + + # system architecture and wordsize +-ARCH = $ARCH ++override ARCH = $ARCH + EndText + + L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH); +@@ -860,7 +877,7 @@ EndText + } + L($F, "PIC = $PIC") if ($PIC); + if ($PKG{LNG} eq 'C') { +- if ($TOOLS =~ /clang/i) { ++ if ($OSTYPE =~ /darwin/i) { + L($F, 'SONAME = -install_name ' . + '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); + L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\'); +@@ -884,7 +901,7 @@ EndText + } + } + if ($PKG{LNG} eq 'C') { +- L($F, "CFLAGS = \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL"); ++ L($F, "CFLAGS += \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL"); + } + L($F, "LDFLAGS = $LDFLAGS") if ($LDFLAGS); + +@@ -970,7 +987,7 @@ EndText + L($F, '# directory rules'); + if ($PKG{LNG} eq 'C') { + L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) ' +- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):'); ++ . '$(OBJDIR) $(INST_LIBDIR):'); + T($F, 'mkdir -p $@'); + } elsif ($PKG{LNG} eq 'JAVA') { + # test if we have jni header path +@@ -1000,12 +1017,12 @@ EndText + L($F, 'export CONFIGURE_FOUND_XML2'); + L($F); + +- if ($OS eq 'linux' || $OS eq 'mac') { ++ if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') { + L($F, '# installation rules'); + L($F, +- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)'); ++ '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)'); + T($F, '@ echo -n "installing \'$(@F)\'... "'); +- T($F, '@ if cp $^ $@ && chmod 644 $@; \\'); ++ T($F, '@ if $(BSD_INSTALL_DATA) $^ $@; \\'); + T($F, ' then \\'); + T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' + . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) ' +@@ -1014,7 +1031,7 @@ EndText + T($F, ' ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) ' + . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\'); + T($F, ' ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' . +- '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));' ++ '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));' + . ' \\'); + T($F, ' echo success; \\'); + T($F, ' else \\'); +@@ -1024,15 +1041,15 @@ EndText + L($F); + + L($F, +- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)'); ++ '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)'); + T($F, '@ echo -n "installing \'$(@F)\'... "'); +- T($F, '@ if cp $^ $@ && chmod 755 $@; \\'); ++ T($F, '@ if $(BSD_INSTALL_LIB) $^ $@; \\'); + T($F, ' then \\'); + if ($OS ne 'mac') { + T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' + . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@); \\'); + } +- if ($OS eq 'linux') { ++ if ($OS eq 'linux' || $OS eq 'bsd') { + T($F, ' ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\'); + } elsif ($OS eq 'mac') { + T($F, ' ln -sf $(@F) ' +@@ -1051,7 +1068,7 @@ EndText + + L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)'); + T($F, '@ echo -n "installing \'$(@F)\'... "'); +- T($F, '@ if cp $^ $@ && chmod 755 $@; \\'); ++ T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@; \\'); + T($F, ' then \\'); + T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' + . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@); \\'); +@@ -1333,7 +1350,7 @@ sub find_in_dir { + ++$found; + } + if (! $found) { +- my $libdir = File::Spec->catdir($dir, 'lib' . $BITS); ++ my $libdir = File::Spec->catdir($dir, 'lib'); + my $f = File::Spec->catdir($libdir, $lib); + print "\tchecking $f\n\t" if ($OPT{'debug'}); + if (-e $f) { Property changes on: biology/ngs-sdk/files/patch-setup_konfigure.perl ___________________________________________________________________ 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: biology/ngs-sdk/files/patch-setup_os-arch.prl =================================================================== --- biology/ngs-sdk/files/patch-setup_os-arch.prl (nonexistent) +++ biology/ngs-sdk/files/patch-setup_os-arch.prl (working copy) @@ -0,0 +1,20 @@ +--- setup/os-arch.prl.orig 2016-10-07 21:59:36 UTC ++++ setup/os-arch.prl +@@ -11,6 +11,8 @@ sub OsArch { + chomp $UNAME; + if ($UNAME =~ /Darwin/) { + $HOST_OS = 'mac'; ++ } elsif ($UNAME =~ /.*BSD/) { ++ $HOST_OS = 'bsd'; + } elsif ($UNAME =~ /Linux/) { + $HOST_OS = 'linux'; + } elsif ($UNAME =~ /SunOS/) { +@@ -49,6 +51,8 @@ sub OsArch { + } + } elsif ($MARCH =~ /x86_64/) { + $HOST_ARCH = 'x86_64'; ++ } elsif ($MARCH =~ /amd64/) { ++ $HOST_ARCH = 'x86_64'; + } elsif ($MARCH =~ /i86pc/) { + $HOST_ARCH = 'x86_64'; + @ARCHITECTURES = qw(x86_64 i386); Property changes on: biology/ngs-sdk/files/patch-setup_os-arch.prl ___________________________________________________________________ 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: biology/ngs-sdk/pkg-descr =================================================================== --- biology/ngs-sdk/pkg-descr (nonexistent) +++ biology/ngs-sdk/pkg-descr (working copy) @@ -0,0 +1,14 @@ +NGS is NCBI's 'front-end' API for accessing reads, alignments and pileups +produced from Next Generation Sequencing. The 'back-end' engine are provided +by biology/ncbi-vdb port. + +Although the GitHub repository contains C++, Java and Python libraries, +this port only install the following libraries to simplify dependencies. + +libngs-c++.a C++ front-end API +libngs-adapt-c++.a C++ adapter for C-based protocol to back-end engine +libngs-sdk.so Java and Python language bindings of the front-end API + +See ${WRKSRC}/CONTENTS for the detail. + +WWW: https://github.com/ncbi/ngs/wiki Property changes on: biology/ngs-sdk/pkg-descr ___________________________________________________________________ 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: biology/ngs-sdk/pkg-plist =================================================================== --- biology/ngs-sdk/pkg-plist (nonexistent) +++ biology/ngs-sdk/pkg-plist (working copy) @@ -0,0 +1,109 @@ +include/ngs/Alignment.hpp +include/ngs/AlignmentIterator.hpp +include/ngs/ErrorMsg.hpp +include/ngs/Fragment.hpp +include/ngs/FragmentIterator.hpp +include/ngs/Package.hpp +include/ngs/Pileup.hpp +include/ngs/PileupEvent.hpp +include/ngs/PileupEventIterator.hpp +include/ngs/PileupIterator.hpp +include/ngs/Read.hpp +include/ngs/ReadCollection.hpp +include/ngs/ReadGroup.hpp +include/ngs/ReadGroupIterator.hpp +include/ngs/ReadIterator.hpp +include/ngs/Reference.hpp +include/ngs/ReferenceIterator.hpp +include/ngs/ReferenceSequence.hpp +include/ngs/Statistics.hpp +include/ngs/StringRef.hpp +include/ngs/adapter/AlignmentItf.hpp +include/ngs/adapter/ErrorMsg.hpp +include/ngs/adapter/FragmentItf.hpp +include/ngs/adapter/PileupEventItf.hpp +include/ngs/adapter/PileupItf.hpp +include/ngs/adapter/ReadCollectionItf.hpp +include/ngs/adapter/ReadGroupItf.hpp +include/ngs/adapter/ReadItf.hpp +include/ngs/adapter/Refcount.hpp +include/ngs/adapter/ReferenceItf.hpp +include/ngs/adapter/ReferenceSequenceItf.hpp +include/ngs/adapter/StatisticsItf.hpp +include/ngs/adapter/StringItf.hpp +include/ngs/adapter/defs.h +include/ngs/inl/Alignment.hpp +include/ngs/inl/AlignmentIterator.hpp +include/ngs/inl/Fragment.hpp +include/ngs/inl/FragmentIterator.hpp +include/ngs/inl/Package.hpp +include/ngs/inl/Pileup.hpp +include/ngs/inl/PileupEvent.hpp +include/ngs/inl/PileupEventIterator.hpp +include/ngs/inl/PileupIterator.hpp +include/ngs/inl/Read.hpp +include/ngs/inl/ReadCollection.hpp +include/ngs/inl/ReadGroup.hpp +include/ngs/inl/ReadGroupIterator.hpp +include/ngs/inl/ReadIterator.hpp +include/ngs/inl/Reference.hpp +include/ngs/inl/ReferenceIterator.hpp +include/ngs/inl/ReferenceSequence.hpp +include/ngs/inl/Statistics.hpp +include/ngs/inl/StringRef.hpp +include/ngs/itf/AlignmentItf.h +include/ngs/itf/AlignmentItf.hpp +include/ngs/itf/ErrBlock.h +include/ngs/itf/ErrBlock.hpp +include/ngs/itf/ErrorMsg.hpp +include/ngs/itf/FragmentItf.h +include/ngs/itf/FragmentItf.hpp +include/ngs/itf/PackageItf.hpp +include/ngs/itf/PileupEventItf.h +include/ngs/itf/PileupEventItf.hpp +include/ngs/itf/PileupItf.h +include/ngs/itf/PileupItf.hpp +include/ngs/itf/ReadCollectionItf.h +include/ngs/itf/ReadCollectionItf.hpp +include/ngs/itf/ReadGroupItf.h +include/ngs/itf/ReadGroupItf.hpp +include/ngs/itf/ReadItf.h +include/ngs/itf/ReadItf.hpp +include/ngs/itf/Refcount.h +include/ngs/itf/Refcount.hpp +include/ngs/itf/ReferenceItf.h +include/ngs/itf/ReferenceItf.hpp +include/ngs/itf/ReferenceSequenceItf.h +include/ngs/itf/ReferenceSequenceItf.hpp +include/ngs/itf/StatisticsItf.h +include/ngs/itf/StatisticsItf.hpp +include/ngs/itf/StringItf.h +include/ngs/itf/StringItf.hpp +include/ngs/itf/VTable.h +include/ngs/itf/VTable.hpp +include/ngs/itf/defs.h +include/ngs/unix/fat86/atomic32.h +include/ngs/unix/i386/atomic32.h +include/ngs/unix/x86_64/atomic32.h +include/ngs/win/atomic32.h +include/ngs/win/stdbool.h +lib/libngs-adapt-c++-static.a +lib/libngs-adapt-c++.a +lib/libngs-adapt-c++.a.1 +lib/libngs-adapt-c++.a.1.3.0 +lib/libngs-c++-static.a +lib/libngs-c++.a +lib/libngs-c++.a.1 +lib/libngs-c++.a.1.3.0 +lib/libngs-sdk.so +lib/libngs-sdk.so.1 +lib/libngs-sdk.so.1.3.0 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FastqTableDump.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.config +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp Property changes on: biology/ngs-sdk/pkg-plist ___________________________________________________________________ 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