[med-svn] [freebayes] 02/06: Fix some linker flags
Andreas Tille
tille at debian.org
Fri Jan 13 16:10:10 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository freebayes.
commit bf1c2d6dccd3a92ee99126353a30decaaf735272
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 8 11:31:01 2016 +0100
Fix some linker flags
---
debian/control | 1 +
debian/patches/use_debian_packaged_vcflib.patch | 90 +++++++++++--------------
2 files changed, 39 insertions(+), 52 deletions(-)
diff --git a/debian/control b/debian/control
index 52eb4dd..e58d174 100644
--- a/debian/control
+++ b/debian/control
@@ -6,6 +6,7 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
cmake,
+ pkg-config,
zlib1g-dev,
libbamtools-dev,
libvcflib-dev,
diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch
index e57706f..dd907a8 100644
--- a/debian/patches/use_debian_packaged_vcflib.patch
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -2,11 +2,9 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 22 Jun 2016 14:36:13 +0200
Description: vcflib needs to be packaged separately
-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 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -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
@@ -14,12 +12,12 @@ Index: b/src/Makefile
-
-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
-+INCLUDE = -I/usr/include/bamtools -I../ttmath -I/usr/include/vcflib -I/usr/include/intervaltree -I/usr/include/smithwaterman
++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
-@@ -57,15 +55,7 @@
+@@ -57,15 +55,7 @@ OBJECTS=BedReader.o \
Bias.o \
Contamination.o \
NonCall.o \
@@ -36,7 +34,7 @@ Index: b/src/Makefile
HEADERS=multichoose.h version_git.h
-@@ -173,17 +163,6 @@
+@@ -173,17 +163,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp
IndelAllele.o: IndelAllele.cpp IndelAllele.h
$(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp
@@ -54,27 +52,23 @@ Index: b/src/Makefile
VERSION_FILE=./version_git.h
RELEASED_VERSION_FILE=./version_release.txt
-@@ -257,5 +236,4 @@
+@@ -257,5 +236,4 @@ autoversion:
clean:
rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
- cd ../vcflib/smithwaterman && make clean
-Index: b/Makefile
-===================================================================
---- a/Makefile 2016-11-05 13:27:24.312784750 +0100
-+++ b/Makefile 2016-11-05 13:27:24.308785595 +0100
+--- a/Makefile
++++ b/Makefile
@@ -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 @@
+--- 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);
@@ -83,7 +77,7 @@ Index: b/src/AlleleParser.cpp
usingVariantInputAlleles = true;
// get sample names from VCF input file
-@@ -1108,7 +1108,7 @@
+@@ -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
@@ -92,7 +86,7 @@ Index: b/src/AlleleParser.cpp
while (haplotypeVariantInputFile.getNextVariant(var)) {
//cerr << "input variant: " << var << endl;
-@@ -1122,9 +1122,9 @@
+@@ -1122,9 +1122,9 @@ void AlleleParser::updateHaplotypeBasisA
}
*/
@@ -105,7 +99,7 @@ Index: b/src/AlleleParser.cpp
//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 @@
+@@ -2107,7 +2107,7 @@ void AlleleParser::getInputVariantsInReg
if (!usingVariantInputAlleles) return;
// get the variants in the target region
@@ -114,7 +108,7 @@ Index: b/src/AlleleParser.cpp
if (!seq.empty()) {
variantCallInputFile.setRegion(seq, start, end);
}
-@@ -2117,10 +2117,10 @@
+@@ -2117,10 +2117,10 @@ void AlleleParser::getInputVariantsInReg
long int pos = currentVariant->position - 1;
// get alternate alleles
bool includePreviousBaseForIndels = true;
@@ -128,7 +122,7 @@ Index: b/src/AlleleParser.cpp
for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) {
orderedVariantAlleles.push_back(variantAlleles[*a]);
}
-@@ -2128,14 +2128,14 @@
+@@ -2128,14 +2128,14 @@ void AlleleParser::getInputVariantsInReg
vector<Allele> genotypeAlleles;
set<long int> alternatePositions;
@@ -147,7 +141,7 @@ Index: b/src/AlleleParser.cpp
long int allelePos = variant.position - 1;
AlleleType type;
string alleleSequence = variant.alt;
-@@ -2240,7 +2240,7 @@
+@@ -2240,7 +2240,7 @@ void AlleleParser::updateInputVariants(l
if (gotRegion) {
// get the variants in the target region
@@ -156,7 +150,7 @@ Index: b/src/AlleleParser.cpp
bool ok;
while (ok = variantCallInputFile.getNextVariant(*currentVariant)) {
-@@ -2248,10 +2248,10 @@
+@@ -2248,10 +2248,10 @@ void AlleleParser::updateInputVariants(l
long int pos = currentVariant->position - 1;
// get alternate alleles
bool includePreviousBaseForIndels = true;
@@ -170,7 +164,7 @@ Index: b/src/AlleleParser.cpp
for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) {
orderedVariantAlleles.push_back(variantAlleles[*a]);
}
-@@ -2259,14 +2259,14 @@
+@@ -2259,14 +2259,14 @@ void AlleleParser::updateInputVariants(l
vector<Allele> genotypeAlleles;
set<long int> alternatePositions;
@@ -189,11 +183,9 @@ Index: b/src/AlleleParser.cpp
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 @@
+--- a/src/AlleleParser.h
++++ b/src/AlleleParser.h
+@@ -163,9 +163,9 @@ public:
BedReader bedReader;
// VCF
@@ -206,7 +198,7 @@ Index: b/src/AlleleParser.h
// input haplotype alleles
//
-@@ -349,7 +349,7 @@
+@@ -349,7 +349,7 @@ private:
int currentRefID;
BamAlignment currentAlignment;
@@ -215,11 +207,9 @@ Index: b/src/AlleleParser.h
};
-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 @@
+--- a/src/ResultData.cpp
++++ b/src/ResultData.cpp
+@@ -5,8 +5,8 @@ using namespace std;
@@ -230,7 +220,7 @@ Index: b/src/ResultData.cpp
BigFloat pHom,
long double bestComboOddsRatio,
//long double alleleSamplingProb,
-@@ -630,8 +630,8 @@
+@@ -630,8 +630,8 @@ vcf::Variant& Results::vcf(
}
@@ -241,11 +231,9 @@ Index: b/src/ResultData.cpp
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 @@
+--- a/src/ResultData.h
++++ b/src/ResultData.h
+@@ -41,8 +41,8 @@ public:
}
}
@@ -256,7 +244,7 @@ Index: b/src/ResultData.h
BigFloat pHom,
long double bestComboOddsRatio,
//long double alleleSamplingProb,
-@@ -61,8 +61,8 @@
+@@ -61,8 +61,8 @@ public:
vector<string>& sequencingTechnologies,
AlleleParser* parser);
@@ -267,11 +255,9 @@ Index: b/src/ResultData.h
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 @@
+--- 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))) {
@@ -280,7 +266,7 @@ Index: b/src/freebayes.cpp
out << results.gvcf(var, nonCalls, parser) << endl;
nonCalls.clear();
}
-@@ -658,12 +658,12 @@
+@@ -658,12 +658,12 @@ int main (int argc, char *argv[]) {
// write the last gVCF record(s)
if (parameters.gVCFout && !nonCalls.empty()) {
@@ -295,7 +281,7 @@ Index: b/src/freebayes.cpp
out << results.vcf(
var,
-@@ -696,7 +696,7 @@
+@@ -696,7 +696,7 @@ int main (int argc, char *argv[]) {
// write the last gVCF record
if (parameters.gVCFout && !nonCalls.empty()) {
Results results;
--
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