This is an automated email from the git hooks/post-receive script. tille pushed a commit to tag debian/1.0.2-1 in repository freebayes.
commit 9cb4df52565f26400f1e0303a7dcde8faeacf23e Author: Andreas Tille <[email protected]> Date: Sat Sep 2 07:41:57 2017 +0200 Commit as uploaded --- debian/patches/fix_test.patch | 8 - debian/patches/series | 3 - debian/patches/use_debian_packaged_bamtools.patch | 68 +++--- debian/patches/use_debian_packaged_vcflib.patch | 271 ++++++++++++++++++++-- 4 files changed, 280 insertions(+), 70 deletions(-) diff --git a/debian/patches/fix_test.patch b/debian/patches/fix_test.patch index 302ed80..a5af80c 100644 --- a/debian/patches/fix_test.patch +++ b/debian/patches/fix_test.patch @@ -13,11 +13,3 @@ Description: vcflib is in a different package - do not test this prove -v t $(freebayes): ---- a/scripts/freebayes-parallel -+++ b/scripts/freebayes-parallel -@@ -37,4 +37,4 @@ command=("freebayes" "$@") - # iterate over regions using gnu parallel to dispatch jobs - cat "$regionsfile" | parallel -k -j "$ncpus" "${command[@]}" --region {} - ) | ../vcflib/scripts/vcffirstheader \ -- | ../vcflib/bin/vcfstreamsort -w 1000 | vcfuniq # remove duplicates at region edges -+ | vcfstreamsort -w 1000 | vcfuniq # remove duplicates at region edges diff --git a/debian/patches/series b/debian/patches/series index 3052e50..e9ae68a 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,6 +1,3 @@ use_debian_packaged_bamtools.patch use_debian_packaged_vcflib.patch -use_debian_packaged_seqlib.patch -use_debian_packaged_libjsoncpp.patch fix_test.patch -vcffirstheader.patch diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch index 9155580..23f035e 100644 --- a/debian/patches/use_debian_packaged_bamtools.patch +++ b/debian/patches/use_debian_packaged_bamtools.patch @@ -4,83 +4,83 @@ Description: Use Debian packaged bamtools --- a/src/Makefile +++ b/src/Makefile -@@ -12,14 +12,13 @@ C=gcc +@@ -12,11 +12,10 @@ C=gcc CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 -BAMTOOLS_ROOT=../bamtools - SEQLIB_ROOT=../SeqLib VCFLIB_ROOT=../vcflib - TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp - HTSLIB_ROOT=$(TABIX_ROOT)/htslib --LIBS = -lz -lm -lpthread --INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib -+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread -+INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib +-LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz -lm +-INCLUDE = -I$(BAMTOOLS_ROOT)/src -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/ ++LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabixpp -lz -lm ++INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/ all: autoversion ../bin/freebayes ../bin/bamleftalign -@@ -37,9 +36,6 @@ gprof: +@@ -34,10 +33,6 @@ gprof: .PHONY: all static debug profiling gprof -# builds bamtools static lib, and copies into root -$(BAMTOOLS_ROOT)/lib/libbamtools.a: - cd $(BAMTOOLS_ROOT) && mkdir -p build && cd build && cmake .. && $(MAKE) - $(HTSLIB_ROOT)/libhts.a: - cd $(HTSLIB_ROOT) && make +- -@@ -78,7 +74,6 @@ OBJECTS=BedReader.o \ + OBJECTS=BedReader.o \ + CNV.o \ +@@ -70,8 +65,7 @@ OBJECTS=BedReader.o \ + ../vcflib/smithwaterman/LeftAlign.o \ ../vcflib/smithwaterman/Repeats.o \ ../vcflib/smithwaterman/IndelAllele.o \ - Variant.o \ -- $(BAMTOOLS_ROOT)/lib/libbamtools.a \ - $(SEQLIB_ROOT)/src/libseqlib.a \ - $(SEQLIB_ROOT)/bwa/libbwa.a \ - $(SEQLIB_ROOT)/fermi-lite/libfml.a \ -@@ -97,10 +92,10 @@ alleles ../bin/alleles: alleles.o $(OBJE +- Variant.o \ +- $(BAMTOOLS_ROOT)/lib/libbamtools.a ++ Variant.o + + HEADERS=multichoose.h version_git.h + +@@ -86,10 +80,10 @@ alleles ../bin/alleles: alleles.o $(OBJE dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS) --bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS) -+bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS) +-bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o +- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS) ++bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o ++ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign -lbamtools --bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS) -+bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS) +-bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamfiltertech.o $(OBJECTS) $(HEADERS) ++bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS) $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS) -@@ -115,7 +110,7 @@ alleles.o: alleles.cpp AlleleParser.o Al +@@ -104,7 +98,7 @@ alleles.o: alleles.cpp AlleleParser.o Al dummy.o: dummy.cpp AlleleParser.o Allele.o $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp --freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a $(BAMTOOLS_ROOT)/lib/libbamtools.a -+freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a +-freebayes.o: freebayes.cpp TryCatch.h $(BAMTOOLS_ROOT)/lib/libbamtools.a ++freebayes.o: freebayes.cpp TryCatch.h $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp fastlz.o: fastlz.c fastlz.h -@@ -136,7 +131,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle +@@ -125,7 +119,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle Ewens.o: Ewens.cpp Ewens.h $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp --AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a -+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a +-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a ++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp Utility.o: Utility.cpp Utility.h Sum.h Product.h -@@ -184,7 +179,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli +@@ -173,7 +167,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli bamfiltertech.o: bamfiltertech.cpp $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp --LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a -+LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a +-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a ++LeftAlign.o: LeftAlign.h LeftAlign.cpp $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp IndelAllele.o: IndelAllele.cpp IndelAllele.h -@@ -275,6 +270,5 @@ autoversion: +@@ -263,6 +257,5 @@ autoversion: clean: rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch index dc36617..dd907a8 100644 --- a/debian/patches/use_debian_packaged_vcflib.patch +++ b/debian/patches/use_debian_packaged_vcflib.patch @@ -4,46 +4,45 @@ Description: vcflib needs to be packaged separately --- a/src/Makefile +++ b/src/Makefile -@@ -13,12 +13,9 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g +@@ -12,10 +12,8 @@ C=gcc + CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 - SEQLIB_ROOT=../SeqLib -VCFLIB_ROOT=../vcflib --TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp --HTSLIB_ROOT=$(TABIX_ROOT)/htslib - --LIBS = -lbamtools -ltabixpp -lz -lm -lpthread --INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib -+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` -+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib +- +-LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabixpp -lz -lm +-INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/ ++LIBS = -lbamtools -ltabixpp -lz -lm -lvcflib `pkg-config --libs libsmithwaterman` ++INCLUDE = -I/usr/include/bamtools -I../ttmath -I/usr/include/vcflib -I/usr/include/intervaltree `pkg-config --cflags libsmithwaterman` -ldisorder all: autoversion ../bin/freebayes ../bin/bamleftalign -@@ -66,14 +63,6 @@ OBJECTS=BedReader.o \ +@@ -57,15 +55,7 @@ OBJECTS=BedReader.o \ + Bias.o \ Contamination.o \ NonCall.o \ - SegfaultHandler.o \ +- SegfaultHandler.o \ - ../vcflib/tabixpp/tabix.o \ -- ../vcflib/tabixpp/htslib/bgzf.o \ +- ../vcflib/tabixpp/bgzf.o \ - ../vcflib/smithwaterman/SmithWatermanGotoh.o \ -- ../vcflib/smithwaterman/disorder.cpp \ +- ../vcflib/smithwaterman/disorder.c \ - ../vcflib/smithwaterman/LeftAlign.o \ - ../vcflib/smithwaterman/Repeats.o \ - ../vcflib/smithwaterman/IndelAllele.o \ -- Variant.o \ - $(SEQLIB_ROOT)/src/libseqlib.a \ - $(SEQLIB_ROOT)/bwa/libbwa.a \ - $(SEQLIB_ROOT)/fermi-lite/libfml.a \ -@@ -185,18 +174,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $ +- Variant.o ++ SegfaultHandler.o + + HEADERS=multichoose.h version_git.h + +@@ -173,17 +163,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp IndelAllele.o: IndelAllele.cpp IndelAllele.h $(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp -Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp - $(CXX) $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp - --../vcflib/tabixpp/tabix.o: -- cd $(TABIX_ROOT)/ && make --../vcflib/tabixpp/htslib/bgzf.o: ../vcflib/tabixpp/htslib/bgzf.c ../vcflib/tabixpp/htslib/htslib/bgzf.h +-../vcflib/tabixpp/tabix.o: ../vcflib/tabixpp/tabix.hpp ../vcflib/tabixpp/tabix.cpp +-../vcflib/tabixpp/bgzf.o: ../vcflib/tabixpp/bgzf.c ../vcflib/tabixpp/bgzf.h - cd ../vcflib/tabixpp && $(MAKE) - -../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp @@ -53,13 +52,11 @@ Description: vcflib needs to be packaged separately VERSION_FILE=./version_git.h RELEASED_VERSION_FILE=./version_release.txt -@@ -269,6 +246,5 @@ autoversion: - +@@ -257,5 +236,4 @@ autoversion: clean: -- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} + rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} - cd ../vcflib/smithwaterman && make clean -+ rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles --- a/Makefile +++ b/Makefile @@ -69,3 +66,227 @@ Description: vcflib needs to be packaged separately cd src && $(MAKE) log: src/version_git.h +--- a/src/AlleleParser.cpp ++++ b/src/AlleleParser.cpp +@@ -485,7 +485,7 @@ void AlleleParser::setupVCFInput(void) { + // variant input for analysis and targeting + if (!parameters.variantPriorsFile.empty()) { + variantCallInputFile.open(parameters.variantPriorsFile); +- currentVariant = new vcf::Variant(variantCallInputFile); ++ currentVariant = new vcflib::Variant(variantCallInputFile); + usingVariantInputAlleles = true; + + // get sample names from VCF input file +@@ -1108,7 +1108,7 @@ void AlleleParser::updateHaplotypeBasisA + pos + referenceLength + CACHED_BASIS_HAPLOTYPE_WINDOW + 1)) { + //cerr << "the vcf line " << haplotypeVariantInputFile.line << endl; + // get the variants in the target region +- vcf::Variant var(haplotypeVariantInputFile); ++ vcflib::Variant var(haplotypeVariantInputFile); + while (haplotypeVariantInputFile.getNextVariant(var)) { + //cerr << "input variant: " << var << endl; + +@@ -1122,9 +1122,9 @@ void AlleleParser::updateHaplotypeBasisA + } + */ + +- map<string, vector<vcf::VariantAllele> > variants = var.parsedAlternates(); +- for (map<string, vector<vcf::VariantAllele> >::iterator a = variants.begin(); a != variants.end(); ++a) { +- for (vector<vcf::VariantAllele>::iterator v = a->second.begin(); v != a->second.end(); ++v) { ++ map<string, vector<vcflib::VariantAllele> > variants = var.parsedAlternates(); ++ for (map<string, vector<vcflib::VariantAllele> >::iterator a = variants.begin(); a != variants.end(); ++a) { ++ for (vector<vcflib::VariantAllele>::iterator v = a->second.begin(); v != a->second.end(); ++v) { + //cerr << v->ref << "/" << v->alt << endl; + if (v->ref != v->alt) { + //cerr << "basis allele " << v->position << " " << v->ref << "/" << v->alt << endl; +@@ -2107,7 +2107,7 @@ void AlleleParser::getInputVariantsInReg + if (!usingVariantInputAlleles) return; + + // get the variants in the target region +- vcf::Variant var(variantCallInputFile); ++ vcflib::Variant var(variantCallInputFile); + if (!seq.empty()) { + variantCallInputFile.setRegion(seq, start, end); + } +@@ -2117,10 +2117,10 @@ void AlleleParser::getInputVariantsInReg + long int pos = currentVariant->position - 1; + // get alternate alleles + bool includePreviousBaseForIndels = true; +- map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->parsedAlternates(); ++ map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->parsedAlternates(); + // TODO this would be a nice option: why does it not work? +- //map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->flatAlternates(); +- vector< vector<vcf::VariantAllele> > orderedVariantAlleles; ++ //map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->flatAlternates(); ++ vector< vector<vcflib::VariantAllele> > orderedVariantAlleles; + for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) { + orderedVariantAlleles.push_back(variantAlleles[*a]); + } +@@ -2128,14 +2128,14 @@ void AlleleParser::getInputVariantsInReg + vector<Allele> genotypeAlleles; + set<long int> alternatePositions; + +- for (vector< vector<vcf::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) { ++ for (vector< vector<vcflib::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) { + +- vector<vcf::VariantAllele>& altAllele = *g; ++ vector<vcflib::VariantAllele>& altAllele = *g; + + vector<Allele> alleles; + +- for (vector<vcf::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) { +- vcf::VariantAllele& variant = *v; ++ for (vector<vcflib::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) { ++ vcflib::VariantAllele& variant = *v; + long int allelePos = variant.position - 1; + AlleleType type; + string alleleSequence = variant.alt; +@@ -2240,7 +2240,7 @@ void AlleleParser::updateInputVariants(l + if (gotRegion) { + + // get the variants in the target region +- vcf::Variant var(variantCallInputFile); ++ vcflib::Variant var(variantCallInputFile); + bool ok; + while (ok = variantCallInputFile.getNextVariant(*currentVariant)) { + +@@ -2248,10 +2248,10 @@ void AlleleParser::updateInputVariants(l + long int pos = currentVariant->position - 1; + // get alternate alleles + bool includePreviousBaseForIndels = true; +- map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->parsedAlternates(); ++ map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->parsedAlternates(); + // TODO this would be a nice option: why does it not work? +- //map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->flatAlternates(); +- vector< vector<vcf::VariantAllele> > orderedVariantAlleles; ++ //map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->flatAlternates(); ++ vector< vector<vcflib::VariantAllele> > orderedVariantAlleles; + for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) { + orderedVariantAlleles.push_back(variantAlleles[*a]); + } +@@ -2259,14 +2259,14 @@ void AlleleParser::updateInputVariants(l + vector<Allele> genotypeAlleles; + set<long int> alternatePositions; + +- for (vector< vector<vcf::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) { ++ for (vector< vector<vcflib::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) { + +- vector<vcf::VariantAllele>& altAllele = *g; ++ vector<vcflib::VariantAllele>& altAllele = *g; + + vector<Allele> alleles; + +- for (vector<vcf::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) { +- vcf::VariantAllele& variant = *v; ++ for (vector<vcflib::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) { ++ vcflib::VariantAllele& variant = *v; + long int allelePos = variant.position - 1; + AlleleType type; + string alleleSequence = variant.alt; +--- a/src/AlleleParser.h ++++ b/src/AlleleParser.h +@@ -163,9 +163,9 @@ public: + BedReader bedReader; + + // VCF +- vcf::VariantCallFile variantCallFile; +- vcf::VariantCallFile variantCallInputFile; // input variant alleles, to target analysis +- vcf::VariantCallFile haplotypeVariantInputFile; // input alleles which will be used to construct haplotype alleles ++ vcflib::VariantCallFile variantCallFile; ++ vcflib::VariantCallFile variantCallInputFile; // input variant alleles, to target analysis ++ vcflib::VariantCallFile haplotypeVariantInputFile; // input alleles which will be used to construct haplotype alleles + + // input haplotype alleles + // +@@ -349,7 +349,7 @@ private: + + int currentRefID; + BamAlignment currentAlignment; +- vcf::Variant* currentVariant; ++ vcflib::Variant* currentVariant; + + }; + +--- a/src/ResultData.cpp ++++ b/src/ResultData.cpp +@@ -5,8 +5,8 @@ using namespace std; + + + +-vcf::Variant& Results::vcf( +- vcf::Variant& var, // variant to update ++vcflib::Variant& Results::vcf( ++ vcflib::Variant& var, // variant to update + BigFloat pHom, + long double bestComboOddsRatio, + //long double alleleSamplingProb, +@@ -630,8 +630,8 @@ vcf::Variant& Results::vcf( + } + + +-vcf::Variant& Results::gvcf( +- vcf::Variant& var, ++vcflib::Variant& Results::gvcf( ++ vcflib::Variant& var, + NonCalls& nonCalls, + AlleleParser* parser) { + +--- a/src/ResultData.h ++++ b/src/ResultData.h +@@ -41,8 +41,8 @@ public: + } + } + +- vcf::Variant& vcf( +- vcf::Variant& var, // variant to update ++ vcflib::Variant& vcf( ++ vcflib::Variant& var, // variant to update + BigFloat pHom, + long double bestComboOddsRatio, + //long double alleleSamplingProb, +@@ -61,8 +61,8 @@ public: + vector<string>& sequencingTechnologies, + AlleleParser* parser); + +- vcf::Variant& gvcf( +- vcf::Variant& var, ++ vcflib::Variant& gvcf( ++ vcflib::Variant& var, + NonCalls& noncalls, + AlleleParser* parser); + }; +--- a/src/freebayes.cpp ++++ b/src/freebayes.cpp +@@ -144,7 +144,7 @@ int main (int argc, char *argv[]) { + || (parameters.gVCFchunk && + nonCalls.lastPos().second - nonCalls.firstPos().second + > parameters.gVCFchunk))) { +- vcf::Variant var(parser->variantCallFile); ++ vcflib::Variant var(parser->variantCallFile); + out << results.gvcf(var, nonCalls, parser) << endl; + nonCalls.clear(); + } +@@ -658,12 +658,12 @@ int main (int argc, char *argv[]) { + + // write the last gVCF record(s) + if (parameters.gVCFout && !nonCalls.empty()) { +- vcf::Variant var(parser->variantCallFile); ++ vcflib::Variant var(parser->variantCallFile); + out << results.gvcf(var, nonCalls, parser) << endl; + nonCalls.clear(); + } + +- vcf::Variant var(parser->variantCallFile); ++ vcflib::Variant var(parser->variantCallFile); + + out << results.vcf( + var, +@@ -696,7 +696,7 @@ int main (int argc, char *argv[]) { + // write the last gVCF record + if (parameters.gVCFout && !nonCalls.empty()) { + Results results; +- vcf::Variant var(parser->variantCallFile); ++ vcflib::Variant var(parser->variantCallFile); + out << results.gvcf(var, nonCalls, parser) << endl; + nonCalls.clear(); + } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
