diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index ce0cdd503e41..87cf159dd0ba 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,56 +1,33 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.0-rc1-130 -PORTREVISION= 1 -DISTVERSIONSUFFIX= -g7e3d806 +DISTVERSION= 1.0.2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ library and CLI tools for parsing and manipulating VCF files LICENSE= MIT -BROKEN_aarch64= fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? +# Should be rechecked since upgrade to 1.0.2. Same error resolved on aarch64. BROKEN_riscv64= fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? LIB_DEPENDS= libhts.so:biology/htslib \ - libtabix.so:biology/tabixpp \ - libsw.so:biology/smithwaterman -COMMON_DEPENDS= fastahack:biology/fastahack \ - filevercmp:sysutils/filevercmp \ - fsom:science/fsom \ - multichoose>=1.0.3:math/multichoose \ - interval_tree_test:math/intervaltree -BUILD_DEPENDS= ${COMMON_DEPENDS} -RUN_DEPENDS= ${COMMON_DEPENDS} + libtabix.so:biology/tabixpp -USES= gmake shebangfix -USE_LDCONFIG= yes +USES= cmake localbase:ldflags pkgconfig shebangfix USE_GITHUB= yes GH_ACCOUNT= ekg - -CXXFLAGS+= -I${LOCALBASE}/include/smithwaterman \ - -I${LOCALBASE}/include/multichoose \ - -I${LOCALBASE}/include/filevercmp \ - -I${LOCALBASE}/include/fastahack \ - -I${LOCALBASE}/include/intervaltree \ - -DVERSION='\"${PORTVERSION}\"' +GH_TUPLE= ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \ + ekg:multichoose:68733cd:multichoose/multichoose \ + ekg:fastahack:bb33265:fastahack/fastahack \ + ekg:intervaltree:17ddd57:intervaltree/intervaltree \ + ekg:fsom:a6ef318:fsom/fsom \ + ekg:filevercmp:1a9b779:filevercmp/filevercmp \ + google:googletest:d225acc:googletest/googletest \ + edawson:libVCFH:615a06b:libVCFH/libVCFH \ + simd-everywhere:simde-no-tests:2931676:simd/src/simde # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 -MAKEFILE= ${FILESDIR}/Makefile.external-libs -INSTALL_TARGET= install-strip - -.include - -.if ${ARCH} == powerpc64le -CFLAGS+= -DNO_WARN_X86_INTRINSICS -USES+= compiler:gcc-c++11-lib -.endif - -post-install: - ${RLN} ${STAGEDIR}${PREFIX}/lib/libvcflib.so.1 \ - ${STAGEDIR}${PREFIX}/lib/libvcflib.so - .include diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index 985916a8d85b..6483bb55115d 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,3 +1,21 @@ -TIMESTAMP = 1523243322 -SHA256 (ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz) = 8ec24354dfc7a87c011c865ab75f3eb72646768ab9cb6eff4263e69763338478 -SIZE (ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz) = 20138644 +TIMESTAMP = 1635902784 +SHA256 (ekg-vcflib-v1.0.2_GH0.tar.gz) = a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910 +SIZE (ekg-vcflib-v1.0.2_GH0.tar.gz) = 19215813 +SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce +SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 +SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297 +SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558 +SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a +SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 +SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1 +SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488 +SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b +SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686 +SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070 +SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053 +SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa +SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815 +SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223 +SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295 +SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63 +SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996 diff --git a/biology/vcflib/files/Makefile.external-libs b/biology/vcflib/files/Makefile.external-libs deleted file mode 100644 index ae030a517b44..000000000000 --- a/biology/vcflib/files/Makefile.external-libs +++ /dev/null @@ -1,207 +0,0 @@ -#OBJ_DIR = ./ -HEADERS = src/Variant.h \ - src/split.h \ - src/pdflib.hpp \ - src/var.hpp \ - src/cdflib.hpp \ - src/rnglib.hpp \ - src/join.h -SOURCES = src/Variant.cpp \ - src/rnglib.cpp \ - src/var.cpp \ - src/pdflib.cpp \ - src/cdflib.cpp \ - src/split.cpp -OBJECTS= $(SOURCES:.cpp=.o) - -VCF_LIB_LOCAL:=$(shell pwd) -BIN_DIR:=bin -LIB_DIR:=lib -SRC_DIR=src -INC_DIR:=include -OBJ_DIR:=obj - -LIB = libvcflib.a -SOVERSION = 1 -SLIB = libvcflib.so.$(SOVERSION) - -# TODO -#vcfstats.cpp - -BIN_SOURCES = src/vcfecho.cpp \ - src/vcfnormalizesvs.cpp \ - src/dumpContigsFromHeader.cpp \ - src/bFst.cpp \ - src/pVst.cpp \ - src/hapLrt.cpp \ - src/popStats.cpp \ - src/wcFst.cpp \ - src/iHS.cpp \ - src/segmentFst.cpp \ - src/segmentIhs.cpp \ - src/genotypeSummary.cpp \ - src/sequenceDiversity.cpp \ - src/pFst.cpp \ - src/smoother.cpp \ - src/LD.cpp \ - src/plotHaps.cpp \ - src/abba-baba.cpp \ - src/permuteGPAT++.cpp \ - src/permuteSmooth.cpp \ - src/normalize-iHS.cpp \ - src/meltEHH.cpp \ - src/vcfaltcount.cpp \ - src/vcfhetcount.cpp \ - src/vcfhethomratio.cpp \ - src/vcffilter.cpp \ - src/vcf2tsv.cpp \ - src/vcfgenotypes.cpp \ - src/vcfannotategenotypes.cpp \ - src/vcfcommonsamples.cpp \ - src/vcfremovesamples.cpp \ - src/vcfkeepsamples.cpp \ - src/vcfsamplenames.cpp \ - src/vcfgenotypecompare.cpp \ - src/vcffixup.cpp \ - src/vcfclassify.cpp \ - src/vcfsamplediff.cpp \ - src/vcfremoveaberrantgenotypes.cpp \ - src/vcfrandom.cpp \ - src/vcfparsealts.cpp \ - src/vcfstats.cpp \ - src/vcfflatten.cpp \ - src/vcfprimers.cpp \ - src/vcfnumalt.cpp \ - src/vcfcleancomplex.cpp \ - src/vcfintersect.cpp \ - src/vcfannotate.cpp \ - src/vcfallelicprimitives.cpp \ - src/vcfoverlay.cpp \ - src/vcfaddinfo.cpp \ - src/vcfkeepinfo.cpp \ - src/vcfkeepgeno.cpp \ - src/vcfafpath.cpp \ - src/vcfcountalleles.cpp \ - src/vcflength.cpp \ - src/vcfdistance.cpp \ - src/vcfrandomsample.cpp \ - src/vcfentropy.cpp \ - src/vcfglxgt.cpp \ - src/vcfroc.cpp \ - src/vcfcheck.cpp \ - src/vcfstreamsort.cpp \ - src/vcfuniq.cpp \ - src/vcfuniqalleles.cpp \ - src/vcfremap.cpp \ - src/vcf2fasta.cpp \ - src/vcfsitesummarize.cpp \ - src/vcfbreakmulti.cpp \ - src/vcfcreatemulti.cpp \ - src/vcfevenregions.cpp \ - src/vcfcat.cpp \ - src/vcfgenosummarize.cpp \ - src/vcfgenosamplenames.cpp \ - src/vcfgeno2haplo.cpp \ - src/vcfleftalign.cpp \ - src/vcfcombine.cpp \ - src/vcfgeno2alleles.cpp \ - src/vcfindex.cpp \ - src/vcf2dag.cpp \ - src/vcfsample2info.cpp \ - src/vcfqual2info.cpp \ - src/vcfinfo2qual.cpp \ - src/vcfglbound.cpp \ - src/vcfunphase.cpp \ - src/vcfnull2ref.cpp \ - src/vcfinfosummarize.cpp - -# when we can figure out how to build on mac -# src/vcfsom.cpp - -#BINS = $(BIN_SOURCES:.cpp=) -BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=))) -SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=)) -# Use ?= to allow overriding from the env or command-line. - -MAKE ?= make -LOCALBASE ?= /usr/local -LIB_PATH ?= ${LOCALBASE}/lib - -CC ?= cc -CXX ?= c++ -CXXFLAGS ?= -O3 -CFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC -CXXFLAGS += $(CFLAGS) --std=c++11 -#CXXFLAGS += -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual - -DESTDIR ?= stage -PREFIX ?= /usr/local -STRIP ?= strip -INSTALL ?= install -c -MKDIR ?= mkdir -p -AR ?= ar - -SSW = src/ssw.o src/ssw_cpp.o - -INCLUDES = -I${LOCALBASE}/include \ - -I${LOCALBASE}/include/smithwaterman \ - -I${LOCALBASE}/include/multichoose \ - -I${LOCALBASE}/include/fastahack \ - -I${LOCALBASE}/include/intervaltree -LDFLAGS += -L. -lvcflib \ - -L$(LIB_PATH) -lsw -ltabix -lhts -lfastahack -lfilevercmp \ - -lpthread -lz -lm - -all: $(OBJECTS) $(BINS) $(LIB) $(SLIB) - -ssw.o: src/ssw.h -ssw_cpp.o: src/ssw_cpp.h - -openmp: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP" - -profiling: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all - -gprof: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all - -$(OBJECTS): $(SOURCES) $(HEADERS) - $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(CXXFLAGS) - -$(SHORTBINS): - $(MAKE) $(BIN_DIR)/$@ - -$(BINS): $(BIN_SOURCES) $(LIB) $(OBJECTS) $(SSW) pre - $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(CXXFLAGS) $(LDFLAGS) - -$(LIB): $(OBJECTS) $(SSW) - ar rs $(LIB) $(OBJECTS) $(SSW) - -$(SLIB): $(OBJECTS) $(SSW) - $(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJECTS) $(SSW) - -install: all - $(MKDIR) $(DESTDIR)$(PREFIX)/bin - $(MKDIR) $(DESTDIR)$(PREFIX)/include/vcflib - $(MKDIR) $(DESTDIR)$(PREFIX)/lib - $(INSTALL) bin/* $(DESTDIR)$(PREFIX)/bin - $(INSTALL) src/*.h src/*.hpp $(DESTDIR)$(PREFIX)/include/vcflib - $(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib - -install-strip: install - $(STRIP) $(DESTDIR)$(PREFIX)/bin/* $(DESTDIR)$(PREFIX)/lib/$(SLIB) - -test: $(BINS) - @prove -Itests/lib -w tests/*.t - -clean: - rm -f $(BINS) $(OBJECTS) - rm -f ssw_cpp.o ssw.o - rm -f $(LIB) - rm -rf $(BIN_DIR) - -pre: - mkdir -p $(BIN_DIR) - -.PHONY: clean all test pre diff --git a/biology/vcflib/files/Makefile.submod b/biology/vcflib/files/Makefile.submod deleted file mode 100644 index aafad2809a9e..000000000000 --- a/biology/vcflib/files/Makefile.submod +++ /dev/null @@ -1,117 +0,0 @@ -#OBJ_DIR = ./ -HEADERS = src/Variant.h \ - src/split.h \ - src/join.h -SOURCES = src/Variant.cpp \ - src/split.cpp -OBJECTS= $(SOURCES:.cpp=.o) - -VCF_LIB_LOCAL:=$(shell pwd) -BIN_DIR:=bin -LIB_DIR:=lib -SRC_DIR=src -INC_DIR:=include -OBJ_DIR:=obj - -include Makefile.common - -TABIX = tabixpp/tabix.o -FASTAHACK = fastahack/Fasta.o -SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o -REPEATS = smithwaterman/Repeats.o -INDELALLELE = smithwaterman/IndelAllele.o -DISORDER = smithwaterman/disorder.o -LEFTALIGN = smithwaterman/LeftAlign.o -FSOM = fsom/fsom.o -FILEVERCMP = filevercmp/filevercmp.o - -INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib -LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm - - -all: $(OBJECTS) $(BINS) - -CXX ?= c++ -CXXFLAGS ?= -O3 -D_FILE_OFFSET_BITS=64 -#CXXFLAGS = -O2 -#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual - -SSW = src/ssw.o src/ssw_cpp.o - -ssw.o: src/ssw.h -ssw_cpp.o:src/ssw_cpp.h - -openmp: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP" - -profiling: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all - -gprof: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all - -$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) - $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ - -multichoose: pre - cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ - -intervaltree: pre - cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ - -$(TABIX): pre - cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ - -$(SMITHWATERMAN): pre - cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/ - -$(DISORDER): $(SMITHWATERMAN) - -$(REPEATS): $(SMITHWATERMAN) - -$(LEFTALIGN): $(SMITHWATERMAN) - -$(INDELALLELE): $(SMITHWATERMAN) - -$(FASTAHACK): pre - cd fastahack && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/ - -#$(FSOM): -# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm - -$(FILEVERCMP): pre - cd filevercmp && make && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/ - -$(SHORTBINS): pre - $(MAKE) bin/$@ - -$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree - $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) - -libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre - ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX) - cp libvcflib.a $(LIB_DIR) - - -test: $(BINS) - @prove -Itests/lib -w tests/*.t - -pre: - if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi - if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi - if [ ! -d $(INC_DIR) ]; then mkdir -p $(INC_DIR); fi - if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi - -clean: - rm -f $(BINS) $(OBJECTS) - rm -f ssw_cpp.o ssw.o - rm -f libvcflib.a - rm -rf $(BIN_DIR) - rm -rf $(LIB_DIR) - rm -rf $(INC_DIR) - rm -rf $(OBJ_DIR) - cd tabixpp && make clean - cd smithwaterman && make clean - cd fastahack && make clean - -.PHONY: clean all test pre diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..2520c928273e --- /dev/null +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -0,0 +1,11 @@ +--- CMakeLists.txt.orig 2021-11-03 15:07:33 UTC ++++ CMakeLists.txt +@@ -230,7 +230,7 @@ if (NOT BUILD_ONLY_LIB) + foreach(BIN ${BINS}) + add_executable(${BIN} src/${BIN}.cpp) + target_include_directories(${BIN} PUBLIC ${TABIXPP_LIBRARIES} ${HTSLIB_INCLUDE_DIRS}) +- target_link_libraries(${BIN} vcflib tabixpp -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES}) ++ target_link_libraries(${BIN} vcflib tabix -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES}) + endforeach(BIN ${BINS}) + install(TARGETS ${BINS} RUNTIME DESTINATION bin) + endif() diff --git a/biology/vcflib/files/patch-src_cdflib.cpp b/biology/vcflib/files/patch-src_cdflib.cpp deleted file mode 100644 index 84bff432c1ed..000000000000 --- a/biology/vcflib/files/patch-src_cdflib.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- src/cdflib.cpp.orig 2018-03-09 20:31:19 UTC -+++ src/cdflib.cpp -@@ -10040,7 +10040,7 @@ void negative_binomial_cdf_values ( int - 1, 2, 3, - 0, 1, 2 }; - -- if ( n_data < 0 ) -+ if ( *n_data < 0 ) - { - *n_data = 0; - } diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 944045d78581..4aa9ba414bd3 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -1,104 +1,198 @@ -bin/LD bin/abba-baba bin/bFst bin/dumpContigsFromHeader bin/genotypeSummary bin/hapLrt bin/iHS bin/meltEHH bin/normalize-iHS bin/pFst bin/pVst bin/permuteGPAT++ bin/permuteSmooth bin/plotHaps bin/popStats bin/segmentFst bin/segmentIhs bin/sequenceDiversity bin/smoother bin/vcf2dag bin/vcf2fasta bin/vcf2tsv bin/vcfaddinfo bin/vcfafpath bin/vcfallelicprimitives bin/vcfaltcount bin/vcfannotate bin/vcfannotategenotypes bin/vcfbreakmulti bin/vcfcat bin/vcfcheck bin/vcfclassify bin/vcfcleancomplex bin/vcfcombine bin/vcfcommonsamples bin/vcfcountalleles bin/vcfcreatemulti bin/vcfdistance bin/vcfecho bin/vcfentropy bin/vcfevenregions bin/vcffilter bin/vcffixup bin/vcfflatten bin/vcfgeno2alleles bin/vcfgeno2haplo bin/vcfgenosamplenames bin/vcfgenosummarize bin/vcfgenotypecompare bin/vcfgenotypes bin/vcfglbound bin/vcfglxgt bin/vcfhetcount bin/vcfhethomratio bin/vcfindex bin/vcfinfo2qual bin/vcfinfosummarize bin/vcfintersect bin/vcfkeepgeno bin/vcfkeepinfo bin/vcfkeepsamples +bin/vcfld bin/vcfleftalign bin/vcflength -bin/vcfnormalizesvs -bin/vcfnull2ref bin/vcfnumalt bin/vcfoverlay bin/vcfparsealts bin/vcfprimers bin/vcfqual2info bin/vcfrandom bin/vcfrandomsample bin/vcfremap bin/vcfremoveaberrantgenotypes bin/vcfremovesamples bin/vcfroc bin/vcfsample2info bin/vcfsamplediff bin/vcfsamplenames bin/vcfsitesummarize bin/vcfstats bin/vcfstreamsort bin/vcfuniq bin/vcfuniqalleles -bin/vcfunphase bin/wcFst -include/vcflib/BedReader.h -include/vcflib/Variant.h -include/vcflib/cdflib.hpp -include/vcflib/convert.h -include/vcflib/gpatInfo.hpp -include/vcflib/join.h -include/vcflib/mt19937ar.h -include/vcflib/pdflib.hpp -include/vcflib/rnglib.hpp -include/vcflib/split.h -include/vcflib/ssw.hpp -include/vcflib/ssw_cpp.hpp -include/vcflib/var.hpp -include/vcflib/vec128int.h -include/vcflib/veclib_types.h +include/BandedSmithWaterman.h +include/BedReader.h +include/Fasta.h +include/IndelAllele.h +include/IntervalTree.h +include/LargeFileSupport.h +include/LeftAlign.h +include/Mosaik.h +include/Region.h +include/Repeats.h +include/SmithWatermanGotoh.h +include/Variant.h +include/catch.hpp +include/cdflib.hpp +include/convert.h +include/disorder.h +include/filevercmp.h +include/gpatInfo.hpp +include/join.h +include/mt19937ar.h +include/multichoose.h +include/multipermute.h +include/pdflib.hpp +include/rnglib.hpp +include/split.h +include/ssw.hpp +include/ssw_cpp.hpp +include/var.hpp +include/vec128int.h +include/veclib_types.h lib/libvcflib.a -lib/libvcflib.so -lib/libvcflib.so.1 +man/man1/man/abba-baba.1.gz +man/man1/man/bFst.1.gz +man/man1/man/dumpContigsFromHeader.1.gz +man/man1/man/genotypeSummary.1.gz +man/man1/man/hapLrt.1.gz +man/man1/man/iHS.1.gz +man/man1/man/meltEHH.1.gz +man/man1/man/normalize-iHS.1.gz +man/man1/man/pFst.1.gz +man/man1/man/pVst.1.gz +man/man1/man/permuteGPAT++.1.gz +man/man1/man/permuteSmooth.1.gz +man/man1/man/plotHaps.1.gz +man/man1/man/popStats.1.gz +man/man1/man/segmentFst.1.gz +man/man1/man/segmentIhs.1.gz +man/man1/man/sequenceDiversity.1.gz +man/man1/man/smoother.1.gz +man/man1/man/vcf2dag.1.gz +man/man1/man/vcf2fasta.1.gz +man/man1/man/vcf2tsv.1.gz +man/man1/man/vcfaddinfo.1.gz +man/man1/man/vcfafpath.1.gz +man/man1/man/vcfallelicprimitives.1.gz +man/man1/man/vcfaltcount.1.gz +man/man1/man/vcfannotate.1.gz +man/man1/man/vcfannotategenotypes.1.gz +man/man1/man/vcfbreakmulti.1.gz +man/man1/man/vcfcat.1.gz +man/man1/man/vcfcheck.1.gz +man/man1/man/vcfclassify.1.gz +man/man1/man/vcfcleancomplex.1.gz +man/man1/man/vcfcombine.1.gz +man/man1/man/vcfcommonsamples.1.gz +man/man1/man/vcfcountalleles.1.gz +man/man1/man/vcfcreatemulti.1.gz +man/man1/man/vcfdistance.1.gz +man/man1/man/vcfecho.1.gz +man/man1/man/vcfentropy.1.gz +man/man1/man/vcfevenregions.1.gz +man/man1/man/vcffilter.1.gz +man/man1/man/vcffixup.1.gz +man/man1/man/vcfflatten.1.gz +man/man1/man/vcfgeno2alleles.1.gz +man/man1/man/vcfgeno2haplo.1.gz +man/man1/man/vcfgenosamplenames.1.gz +man/man1/man/vcfgenosummarize.1.gz +man/man1/man/vcfgenotypecompare.1.gz +man/man1/man/vcfgenotypes.1.gz +man/man1/man/vcfglbound.1.gz +man/man1/man/vcfglxgt.1.gz 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