[med-svn] [freebayes] 01/01: chorrect use of vcf namespace to vcflib
Gert Wollny
gert-guest at moszumanska.debian.org
Sat Nov 5 12:38:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository freebayes.
commit 224c95457304f1735ce392829e29e765181c7a17
Author: Gert Wollny <gw.fossdev at gmail.com>
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 <tille at debian.org>
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
More information about the debian-med-commit
mailing list