Author: tille Date: 2014-01-01 18:20:56 +0000 (Wed, 01 Jan 2014) New Revision: 15698
Modified: trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools Log: Update patch to use Debian packaged samtools Modified: trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools =================================================================== --- trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools 2014-01-01 18:08:46 UTC (rev 15697) +++ trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools 2014-01-01 18:20:56 UTC (rev 15698) @@ -1,5 +1,9 @@ ---- a/ReadDistribution.h -+++ b/ReadDistribution.h +Author: Tim Booth <[email protected]> +Last-Update: Wed, 01 Jan 2014 19:04:47 +0100 (by Andreas Tille) +Description: link against Debian packaged samtools + +--- BitSeq-0.7.0.orig/ReadDistribution.h ++++ BitSeq-0.7.0/ReadDistribution.h @@ -21,8 +21,8 @@ #else @@ -11,19 +15,37 @@ //#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t))) /* ---- a/Makefile -+++ b/Makefile -@@ -25,11 +25,8 @@ - getWithinGeneExpression: getWithinGeneExpression.cpp common.o ArgumentParser.o TranscriptInfo.o PosteriorSamples.o common.h - $(CXX) $(CXXFLAGS) getWithinGeneExpression.cpp common.o ArgumentParser.o TranscriptInfo.o PosteriorSamples.o -o getWithinGeneExpression +--- BitSeq-0.7.0.orig/Makefile ++++ BitSeq-0.7.0/Makefile +@@ -63,8 +63,8 @@ + getWithinGeneExpression: getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o + $(CXX) $(CXXFLAGS) $(LDFLAGS) getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression --parseAlignment: parseAlignment.cpp common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o samtools/sam.o -- $(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools samtools/*.o common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o parseAlignment.cpp -lz -o parseAlignment -- +-parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/sam.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o +- $(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread -Isamtools parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/*.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -o parseAlignment ++parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o ++ $(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -lbam -o parseAlignment + + transposeLargeFile: transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o + $(CXX) $(CXXFLAGS) $(LDFLAGS) transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o -o transposeLargeFile +@@ -92,7 +92,7 @@ + $(CXX) $(CXXFLAGS) -ffunction-sections -fdata-sections -c PosteriorSamples.cpp + + ReadDistribution.o: ReadDistribution.cpp ReadDistribution.h TranscriptExpression.h TranscriptInfo.h TranscriptSequence.h +- $(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools -c ReadDistribution.cpp ++ $(CXX) $(CXXFLAGS) $(OPENMP) -c ReadDistribution.cpp + + Sampler.o: Sampler.cpp Sampler.h GibbsParameters.h + $(CXX) $(CXXFLAGS) $(BOOSTFLAGS) -c Sampler.cpp +@@ -116,10 +116,7 @@ + asa103/asa103.o: + make --directory asa103 + -samtools/sam.o: - make --directory samtools -+parseAlignment: parseAlignment.cpp common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o -+ $(CXX) $(CXXFLAGS) $(OPENMP) common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o parseAlignment.cpp -lbam -lz -o parseAlignment +- + # CLEAN: + clean: +- rm asa103/*.o samtools/*.o *.o $(PROGRAMS) ++ rm -f asa103/*.o samtools/*.o *.o $(PROGRAMS) - convertSamples: convertSamples.cpp common.o ArgumentParser.o TranscriptInfo.o - $(CXX) $(CXXFLAGS) convertSamples.cpp common.o ArgumentParser.o TranscriptInfo.o -o convertSamples _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
