[med-svn] [freebayes] 05/06: Commit as uploaded
Andreas Tille
tille at debian.org
Sat Sep 2 05:46:08 UTC 2017
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 <tille at debian.org>
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();
+ }
--
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