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commit 224c95457304f1735ce392829e29e765181c7a17 Author: Gert Wollny <[email protected]> Date: Sat Nov 5 13:30:59 2016 +0100 chorrect use of vcf namespace to vcflib --- debian/patches/use_debian_packaged_vcflib.patch | 254 +++++++++++++++++++++++- 1 file changed, 246 insertions(+), 8 deletions(-) diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch index a45c74d..9b55763 100644 --- a/debian/patches/use_debian_packaged_vcflib.patch +++ b/debian/patches/use_debian_packaged_vcflib.patch @@ -2,9 +2,11 @@ Author: Andreas Tille <[email protected]> Last-Update: Wed, 22 Jun 2016 14:36:13 +0200 Description: vcflib needs to be packaged separately ---- a/src/Makefile -+++ b/src/Makefile -@@ -12,10 +12,8 @@ C=gcc +Index: b/src/Makefile +=================================================================== +--- a/src/Makefile 2016-11-05 13:27:24.312784750 +0100 ++++ b/src/Makefile 2016-11-05 13:27:24.308785595 +0100 +@@ -12,10 +12,8 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 @@ -17,7 +19,7 @@ Description: vcflib needs to be packaged separately all: autoversion ../bin/freebayes ../bin/bamleftalign -@@ -57,15 +55,7 @@ OBJECTS=BedReader.o \ +@@ -57,15 +55,7 @@ Bias.o \ Contamination.o \ NonCall.o \ @@ -34,7 +36,7 @@ Description: vcflib needs to be packaged separately HEADERS=multichoose.h version_git.h -@@ -173,17 +163,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp +@@ -173,17 +163,6 @@ IndelAllele.o: IndelAllele.cpp IndelAllele.h $(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp @@ -52,17 +54,253 @@ Description: vcflib needs to be packaged separately VERSION_FILE=./version_git.h RELEASED_VERSION_FILE=./version_release.txt -@@ -257,5 +236,4 @@ autoversion: +@@ -257,5 +236,4 @@ clean: rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} - cd ../vcflib/smithwaterman && make clean ---- a/Makefile -+++ b/Makefile +Index: b/Makefile +=================================================================== +--- a/Makefile 2016-11-05 13:27:24.312784750 +0100 ++++ b/Makefile 2016-11-05 13:27:24.308785595 +0100 @@ -1,4 +1,4 @@ -all: vcflib/Makefile log +all: cd src && $(MAKE) log: src/version_git.h +Index: b/src/AlleleParser.cpp +=================================================================== +--- a/src/AlleleParser.cpp 2016-11-05 13:27:01.774171218 +0100 ++++ b/src/AlleleParser.cpp 2016-11-05 13:29:59.083115001 +0100 +@@ -485,7 +485,7 @@ + // 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 @@ + 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 @@ + } + */ + +- 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 @@ + 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 @@ + 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 @@ + 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 @@ + 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 @@ + 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 @@ + 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; +Index: b/src/AlleleParser.h +=================================================================== +--- a/src/AlleleParser.h 2016-11-05 13:27:01.774171218 +0100 ++++ b/src/AlleleParser.h 2016-11-05 13:29:50.843186281 +0100 +@@ -163,9 +163,9 @@ + 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 @@ + + int currentRefID; + BamAlignment currentAlignment; +- vcf::Variant* currentVariant; ++ vcflib::Variant* currentVariant; + + }; + +Index: b/src/ResultData.cpp +=================================================================== +--- a/src/ResultData.cpp 2016-11-05 13:27:01.778170142 +0100 ++++ b/src/ResultData.cpp 2016-11-05 13:29:31.227560841 +0100 +@@ -5,8 +5,8 @@ + + + +-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::gvcf( +- vcf::Variant& var, ++vcflib::Variant& Results::gvcf( ++ vcflib::Variant& var, + NonCalls& nonCalls, + AlleleParser* parser) { + +Index: b/src/ResultData.h +=================================================================== +--- a/src/ResultData.h 2016-11-05 13:27:01.778170142 +0100 ++++ b/src/ResultData.h 2016-11-05 13:29:16.660047718 +0100 +@@ -41,8 +41,8 @@ + } + } + +- 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 @@ + vector<string>& sequencingTechnologies, + AlleleParser* parser); + +- vcf::Variant& gvcf( +- vcf::Variant& var, ++ vcflib::Variant& gvcf( ++ vcflib::Variant& var, + NonCalls& noncalls, + AlleleParser* parser); + }; +Index: b/src/freebayes.cpp +=================================================================== +--- a/src/freebayes.cpp 2016-11-05 13:27:01.802163691 +0100 ++++ b/src/freebayes.cpp 2016-11-05 13:29:41.163333332 +0100 +@@ -144,7 +144,7 @@ + || (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 @@ + + // 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 @@ + // 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
