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Commits on Source (2)
Fix patch
· 3de08fb5
Andreas Tille
authored
May 23, 2018
3de08fb5
Bump versioned Build-Depends: libseqlib-dev (>= 1.1.2+dfsg)
· a8cea70b
Andreas Tille
authored
May 23, 2018
a8cea70b
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debian/changelog
View file @
a8cea70b
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@@ -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@debian.org> Thu, 26 Apr 2018 15:30:48 +0200
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debian/control
View file @
a8cea70b
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@@ -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,
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debian/patches/use_debian_libs.patch
View file @
a8cea70b
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@@ -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 \
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@@ -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 +7
8
,10 @@
alleles ../bin/alleles: alleles.o $(OBJE
@@ -100,10 +7
7
,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)
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@@ -66,7 +67,7 @@ Description: Use Debian packaged bamtools
$(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
@@ -118,7 +9
6
,7 @@
alleles.o: alleles.cpp AlleleParser.o Al
@@ -118,7 +9
5
,7 @@
alleles.o: alleles.cpp AlleleParser.o Al
dummy.o: dummy.cpp AlleleParser.o Allele.o
$(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp
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@@ -75,7 +76,7 @@ Description: Use Debian packaged bamtools
$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
fastlz.o: fastlz.c fastlz.h
@@ -139,7 +11
7
,7 @@
Genotype.o: Genotype.cpp Genotype.h Alle
@@ -139,7 +11
6
,7 @@
Genotype.o: Genotype.cpp Genotype.h Alle
Ewens.o: Ewens.cpp Ewens.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Ewens.cpp
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@@ -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 +16
5
,12 @@
bamleftalign.o: bamleftalign.cpp LeftAli
@@ -187,22 +16
4
,12 @@
bamleftalign.o: bamleftalign.cpp LeftAli
bamfiltertech.o: bamfiltertech.cpp
$(CXX) $(CXXFLAGS) $(INCLUDE) -c bamfiltertech.cpp
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@@ -108,7 +109,7 @@ Description: Use Debian packaged bamtools
VERSION_FILE=./version_git.h
RELEASED_VERSION_FILE=./version_release.txt
@@ -277,5 +24
5
,3 @@
autoversion:
@@ -277,5 +24
4
,3 @@
autoversion:
clean:
rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
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