Andreas Tille pushed to branch master at Debian Med / freebayes
Commits: 3de08fb5 by Andreas Tille at 2018-05-23T11:33:45+02:00 Fix patch - - - - - a8cea70b by Andreas Tille at 2018-05-23T11:34:38+02:00 Bump versioned Build-Depends: libseqlib-dev (>= 1.1.2+dfsg) - - - - - 3 changed files: - debian/changelog - debian/control - debian/patches/use_debian_libs.patch Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -3,6 +3,7 @@ freebayes (1.2.0-1) UNRELEASED; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 + * Bump versioned Build-Depends: libseqlib-dev (>= 1.1.2+dfsg) -- Andreas Tille <[email protected]> Thu, 26 Apr 2018 15:30:48 +0200 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11~), libbamtools-dev, libvcflib-dev (>= 1.0.0~rc1+dfsg1-4), libtabixpp-dev, - libseqlib-dev (>= 1.1.1+dfsg-4), + libseqlib-dev (>= 1.1.2+dfsg), bc, samtools, parallel, ===================================== debian/patches/use_debian_libs.patch ===================================== --- a/debian/patches/use_debian_libs.patch +++ b/debian/patches/use_debian_libs.patch @@ -34,10 +34,11 @@ Description: Use Debian packaged bamtools OBJECTS=BedReader.o \ CNV.o \ fastlz.o \ -@@ -75,17 +63,7 @@ OBJECTS=BedReader.o \ +@@ -74,18 +62,7 @@ OBJECTS=BedReader.o \ + Bias.o \ Contamination.o \ NonCall.o \ - SegfaultHandler.o \ +- SegfaultHandler.o \ - ../vcflib/tabixpp/tabix.o \ - ../vcflib/smithwaterman/SmithWatermanGotoh.o \ - ../vcflib/smithwaterman/disorder.cpp \ @@ -49,11 +50,11 @@ Description: Use Debian packaged bamtools - $(SEQLIB_ROOT)/bwa/libbwa.a \ - $(SEQLIB_ROOT)/fermi-lite/libfml.a \ - $(SEQLIB_ROOT)/htslib/libhts.a -+ Variant.o ++ SegfaultHandler.o HEADERS=multichoose.h version_git.h -@@ -100,10 +78,10 @@ alleles ../bin/alleles: alleles.o $(OBJE +@@ -100,10 +77,10 @@ alleles ../bin/alleles: alleles.o $(OBJE dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib) $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS) @@ -66,7 +67,7 @@ Description: Use Debian packaged bamtools $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS) -@@ -118,7 +96,7 @@ alleles.o: alleles.cpp AlleleParser.o Al +@@ -118,7 +95,7 @@ alleles.o: alleles.cpp AlleleParser.o Al dummy.o: dummy.cpp AlleleParser.o Allele.o $(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp @@ -75,7 +76,7 @@ Description: Use Debian packaged bamtools $(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp fastlz.o: fastlz.c fastlz.h -@@ -139,7 +117,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle +@@ -139,7 +116,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle Ewens.o: Ewens.cpp Ewens.h $(CXX) $(CXXFLAGS) $(INCLUDE) -c Ewens.cpp @@ -84,7 +85,7 @@ Description: Use Debian packaged bamtools $(CXX) $(CXXFLAGS) $(INCLUDE) -c AlleleParser.cpp Utility.o: Utility.cpp Utility.h Sum.h Product.h -@@ -187,22 +165,12 @@ bamleftalign.o: bamleftalign.cpp LeftAli +@@ -187,22 +164,12 @@ bamleftalign.o: bamleftalign.cpp LeftAli bamfiltertech.o: bamfiltertech.cpp $(CXX) $(CXXFLAGS) $(INCLUDE) -c bamfiltertech.cpp @@ -108,7 +109,7 @@ Description: Use Debian packaged bamtools VERSION_FILE=./version_git.h RELEASED_VERSION_FILE=./version_release.txt -@@ -277,5 +245,3 @@ autoversion: +@@ -277,5 +244,3 @@ autoversion: clean: rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp View it on GitLab: https://salsa.debian.org/med-team/freebayes/compare/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6...a8cea70bc635d3b9c6b07ebbc7fdc13f294f15ef -- View it on GitLab: https://salsa.debian.org/med-team/freebayes/compare/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6...a8cea70bc635d3b9c6b07ebbc7fdc13f294f15ef You're receiving this email because of your account on salsa.debian.org.
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