[med-svn] [Git][med-team/freebayes][master] 2 commits: Fix patch

[Andreas Tille]

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 <tille at debian.org>  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
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