[med-svn] [Git][med-team/freebayes][master] Refresh and restructure patches
Andreas Tille
gitlab at salsa.debian.org
Wed May 23 08:43:18 BST 2018
Andreas Tille pushed to branch master at Debian Med / freebayes
Commits:
cee63932 by Andreas Tille at 2018-05-23T09:35:07+02:00
Refresh and restructure patches
- - - - -
9 changed files:
- + debian/patches/fix_all_target.patch
- − debian/patches/fix_json_name_clash.patch
- debian/patches/series
- debian/patches/use_cpp11.patch
- + debian/patches/use_debian_libs.patch
- − debian/patches/use_debian_packaged_bamtools.patch
- − debian/patches/use_debian_packaged_libjsoncpp.patch
- − debian/patches/use_debian_packaged_seqlib.patch
- − debian/patches/use_debian_packaged_vcflib.patch
Changes:
=====================================
debian/patches/fix_all_target.patch
=====================================
--- /dev/null
+++ b/debian/patches/fix_all_target.patch
@@ -0,0 +1,12 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 22 Jun 2016 14:36:13 +0200
+Description: vcflib needs to be packaged separately
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,4 +1,4 @@
+-all: vcflib/Makefile log
++all:
+ cd src && $(MAKE)
+
+ wbamtools: vcflib/Makefile log
=====================================
debian/patches/fix_json_name_clash.patch deleted
=====================================
--- a/debian/patches/fix_json_name_clash.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: Mon, 4 Sep 2017 12:27:38 +0200
-Acked-by: Andreas Tille <tille at debian.org>
-Description: Fix a "json" name clash
- htslib exports an enum value called `json`. That clashes with the
- definition of a friend function. For simplicity we resolve this by
- renaming the local function and ask htslib to prefix their symbols in
- the future.
-
----
- src/Allele.cpp | 10 +++++-----
- src/Allele.h | 10 +++++-----
- src/Sample.cpp | 2 +-
- 3 files changed, 11 insertions(+), 11 deletions(-)
-
-diff --git a/src/Allele.cpp b/src/Allele.cpp
-index 2c58c79..8645704 100644
---- a/src/Allele.cpp
-+++ b/src/Allele.cpp
-@@ -332,19 +332,19 @@ string stringForAlleles(vector<Allele> &alleles) {
- return out.str();
- }
-
--string json(vector<Allele*> &alleles) {
-+string to_json(vector<Allele*> &alleles) {
- stringstream out;
- vector<Allele*>::iterator a = alleles.begin();
-- out << "[" << (*a)->json(); ++a;
-+ out << "[" << (*a)->to_json(); ++a;
- for (; a != alleles.end(); ++a)
-- out << "," << (*a)->json();
-+ out << "," << (*a)->to_json();
- out << "]";
- return out.str();
- }
-
--string json(Allele*& allele) { return allele->json(); }
-+string to_json(Allele*& allele) { return allele->to_json(); }
-
--string Allele::json(void) {
-+string Allele::to_json(void) {
- stringstream out;
- if (!genotypeAllele) {
- out << "{\"id\":\"" << readID << "\""
-diff --git a/src/Allele.h b/src/Allele.h
-index 3f0125f..ff41c10 100644
---- a/src/Allele.h
-+++ b/src/Allele.h
-@@ -96,10 +96,10 @@ class Allele {
- friend ostream &operator<<(ostream &out, Allele &a);
- friend ostream &operator<<(ostream &out, Allele* &a);
-
-- friend string json(vector<Allele*> &alleles, long int &position);
-- friend string json(vector<Allele*> &alleles);
-- friend string json(Allele &allele, long int &position);
-- friend string json(Allele* &allele);
-+ friend string to_json(vector<Allele*> &alleles, long int &position);
-+ friend string to_json(vector<Allele*> &alleles);
-+ friend string to_json(Allele &allele, long int &position);
-+ friend string to_json(Allele* &allele);
-
- public:
-
-@@ -262,7 +262,7 @@ public:
- // this is used to update cached data in the allele prior to presenting the allele for analysis
- // for the current base, just use allele.currentBase
-
-- string json(void);
-+ string to_json(void);
- unsigned int getLengthOnReference(void);
- int referenceLengthFromCigar(void);
-
-diff --git a/src/Sample.cpp b/src/Sample.cpp
-index 06207cd..a6e3886 100644
---- a/src/Sample.cpp
-+++ b/src/Sample.cpp
-@@ -264,7 +264,7 @@ string Sample::json(void) {
- vector<Allele*>& alleles = g->second;
- for (vector<Allele*>::iterator a = alleles.begin(); a != alleles.end(); ++a) {
- if (!first) { out << ","; } else { first = false; }
-- out << (*a)->json();
-+ out << (*a)->to_json();
- }
- }
- out << "]";
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,8 +1,5 @@
-use_debian_packaged_bamtools.patch
-use_debian_packaged_vcflib.patch
-use_debian_packaged_seqlib.patch
-use_debian_packaged_libjsoncpp.patch
+use_debian_libs.patch
+fix_all_target.patch
fix_test.patch
vcffirstheader.patch
use_cpp11.patch
-fix_json_name_clash.patch
=====================================
debian/patches/use_cpp11.patch
=====================================
--- a/debian/patches/use_cpp11.patch
+++ b/debian/patches/use_cpp11.patch
@@ -6,14 +6,12 @@ Description: Compile as C++11
src/Makefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
-diff --git a/src/Makefile b/src/Makefile
-index 15a6da6..7b3b35a 100644
--- a/src/Makefile
+++ b/src/Makefile
-@@ -9,7 +9,7 @@ CXX=g++
- C=gcc
+@@ -17,7 +17,7 @@ export LIBFLAGS
# Compiler flags
+
-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g -std=gnu++11
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
=====================================
debian/patches/use_debian_libs.patch
=====================================
--- /dev/null
+++ b/debian/patches/use_debian_libs.patch
@@ -0,0 +1,116 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 28 May 2014 21:23:38 +0200
+Description: Use Debian packaged bamtools
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -20,14 +20,8 @@ export LIBFLAGS
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+
+-SEQLIB_ROOT=../SeqLib
+-VCFLIB_ROOT=../vcflib
+-TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
+-HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib
+-
+-LIBS = -lz -llzma -lbz2 -lm -lpthread
+-INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT)
+-#INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`
+
+ all: autoversion ../bin/freebayes ../bin/bamleftalign
+
+@@ -45,12 +39,6 @@ gprof:
+
+ .PHONY: all static debug profiling gprof
+
+-$(HTSLIB_ROOT)/libhts.a:
+- cd $(HTSLIB_ROOT) && make
+-
+-$(SEQLIB_ROOT)/src/libseqlib.a:
+- cd $(SEQLIB_ROOT) && ./configure && make
+-
+ OBJECTS=BedReader.o \
+ CNV.o \
+ fastlz.o \
+@@ -75,17 +63,7 @@ OBJECTS=BedReader.o \
+ Contamination.o \
+ NonCall.o \
+ SegfaultHandler.o \
+- ../vcflib/tabixpp/tabix.o \
+- ../vcflib/smithwaterman/SmithWatermanGotoh.o \
+- ../vcflib/smithwaterman/disorder.cpp \
+- ../vcflib/smithwaterman/LeftAlign.o \
+- ../vcflib/smithwaterman/Repeats.o \
+- ../vcflib/smithwaterman/IndelAllele.o \
+- Variant.o \
+- $(SEQLIB_ROOT)/src/libseqlib.a \
+- $(SEQLIB_ROOT)/bwa/libbwa.a \
+- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+- $(SEQLIB_ROOT)/htslib/libhts.a
++ Variant.o
+
+ HEADERS=multichoose.h version_git.h
+
+@@ -100,10 +78,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
+ dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)
+ $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
+
+-bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
++bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
+ $(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)
+
+-bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
++bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
+ $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
+
+
+@@ -118,7 +96,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
+ dummy.o: dummy.cpp AlleleParser.o Allele.o
+ $(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp
+
+-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a ../vcflib/tabixpp/tabix.o
++freebayes.o: freebayes.cpp TryCatch.h
+ $(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
+
+ fastlz.o: fastlz.c fastlz.h
+@@ -139,7 +117,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
+ Ewens.o: Ewens.cpp Ewens.h
+ $(CXX) $(CXXFLAGS) $(INCLUDE) -c Ewens.cpp
+
+-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
+ $(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
+ bamfiltertech.o: bamfiltertech.cpp
+ $(CXX) $(CXXFLAGS) $(INCLUDE) -c bamfiltertech.cpp
+
+-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
++LeftAlign.o: LeftAlign.h LeftAlign.cpp
+ $(CXX) $(CXXFLAGS) $(INCLUDE) -c LeftAlign.cpp
+
+ IndelAllele.o: IndelAllele.cpp IndelAllele.h
+ $(CXX) $(CXXFLAGS) $(INCLUDE) -c IndelAllele.cpp
+
+-Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp
+- $(CXX) $(CXXFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
+-# $(CXX) -std=c++11 $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
+-
+-../vcflib/tabixpp/tabix.o:
+- cd $(TABIX_ROOT)/ && $(MAKE) && cp tabix.hpp ../../src/
+-
+-../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp
+- cd ../vcflib/smithwaterman && $(MAKE)
+-
+
+ VERSION_FILE=./version_git.h
+ RELEASED_VERSION_FILE=./version_release.txt
+@@ -277,5 +245,3 @@ autoversion:
+
+ clean:
+ rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
+- if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi
+- make -C $(VCFLIB_ROOT)/smithwaterman clean
=====================================
debian/patches/use_debian_packaged_bamtools.patch deleted
=====================================
--- a/debian/patches/use_debian_packaged_bamtools.patch
+++ /dev/null
@@ -1,89 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 28 May 2014 21:23:38 +0200
-Description: Use Debian packaged bamtools
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -12,14 +12,13 @@ C=gcc
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-
--BAMTOOLS_ROOT=../bamtools
- SEQLIB_ROOT=../SeqLib
- VCFLIB_ROOT=../vcflib
- TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
- HTSLIB_ROOT=$(TABIX_ROOT)/htslib
-
--LIBS = -lz -lm -lpthread
--INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
-+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread
-+INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
-
- all: autoversion ../bin/freebayes ../bin/bamleftalign
-
-@@ -37,9 +36,6 @@ gprof:
-
- .PHONY: all static debug profiling gprof
-
--# builds bamtools static lib, and copies into root
--$(BAMTOOLS_ROOT)/lib/libbamtools.a:
-- cd $(BAMTOOLS_ROOT) && mkdir -p build && cd build && cmake .. && $(MAKE)
- $(HTSLIB_ROOT)/libhts.a:
- cd $(HTSLIB_ROOT) && make
-
-@@ -78,7 +74,6 @@ OBJECTS=BedReader.o \
- ../vcflib/smithwaterman/Repeats.o \
- ../vcflib/smithwaterman/IndelAllele.o \
- Variant.o \
-- $(BAMTOOLS_ROOT)/lib/libbamtools.a \
- $(SEQLIB_ROOT)/src/libseqlib.a \
- $(SEQLIB_ROOT)/bwa/libbwa.a \
- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
-@@ -97,10 +92,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
- dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
- $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
-
--bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
-+bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
-
--bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
-+bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
- $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
-
-
-@@ -115,7 +110,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
- dummy.o: dummy.cpp AlleleParser.o Allele.o
- $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
-
--freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
- $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
-
- fastlz.o: fastlz.c fastlz.h
-@@ -136,7 +131,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
- Ewens.o: Ewens.cpp Ewens.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
-
--AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a
-+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
- $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
-
- Utility.o: Utility.cpp Utility.h Sum.h Product.h
-@@ -184,7 +179,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
- bamfiltertech.o: bamfiltertech.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
-
--LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a
-+LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
- $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
-
- IndelAllele.o: IndelAllele.cpp IndelAllele.h
-@@ -275,6 +270,5 @@ autoversion:
-
- clean:
- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
-- cd $(BAMTOOLS_ROOT)/build && make clean
- cd ../vcflib/smithwaterman && make clean
-
=====================================
debian/patches/use_debian_packaged_libjsoncpp.patch deleted
=====================================
--- a/debian/patches/use_debian_packaged_libjsoncpp.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 28 May 2014 21:23:38 +0200
-Description: Use Debian packaged libjsoncpp
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -12,8 +12,8 @@ C=gcc
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-
--LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
--INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
-+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
-+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`
-
- all: autoversion ../bin/freebayes ../bin/bamleftalign
-
=====================================
debian/patches/use_debian_packaged_seqlib.patch deleted
=====================================
--- a/debian/patches/use_debian_packaged_seqlib.patch
+++ /dev/null
@@ -1,87 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 28 May 2014 21:23:38 +0200
-Description: Use Debian packaged htslib and seqlib
- carries another copy of htslib - we replace both
-
---- 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
-
--SEQLIB_ROOT=../SeqLib
--
--LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
--INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
-+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
-+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
-
- all: autoversion ../bin/freebayes ../bin/bamleftalign
-
-@@ -33,12 +31,6 @@ gprof:
-
- .PHONY: all static debug profiling gprof
-
--$(HTSLIB_ROOT)/libhts.a:
-- cd $(HTSLIB_ROOT) && make
--
--$(SEQLIB_ROOT)/src/libseqlib.a:
-- cd $(SEQLIB_ROOT) && ./configure && make
--
- OBJECTS=BedReader.o \
- CNV.o \
- fastlz.o \
-@@ -62,11 +54,7 @@ OBJECTS=BedReader.o \
- Bias.o \
- Contamination.o \
- NonCall.o \
-- SegfaultHandler.o \
-- $(SEQLIB_ROOT)/src/libseqlib.a \
-- $(SEQLIB_ROOT)/bwa/libbwa.a \
-- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
-- $(SEQLIB_ROOT)/htslib/libhts.a
-+ SegfaultHandler.o
-
- HEADERS=multichoose.h version_git.h
-
-@@ -81,10 +69,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
- dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
- $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
-
--bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
-+bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)
-
--bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
-+bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
- $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
-
-
-@@ -99,7 +87,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
- dummy.o: dummy.cpp AlleleParser.o Allele.o
- $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
-
--freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
-+freebayes.o: freebayes.cpp TryCatch.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
-
- fastlz.o: fastlz.c fastlz.h
-@@ -120,7 +108,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
- Ewens.o: Ewens.cpp Ewens.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
-
--AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
-+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
-
- Utility.o: Utility.cpp Utility.h Sum.h Product.h
-@@ -168,7 +156,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
- bamfiltertech.o: bamfiltertech.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
-
--LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
-+LeftAlign.o: LeftAlign.h LeftAlign.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
-
- IndelAllele.o: IndelAllele.cpp IndelAllele.h
=====================================
debian/patches/use_debian_packaged_vcflib.patch deleted
=====================================
--- a/debian/patches/use_debian_packaged_vcflib.patch
+++ /dev/null
@@ -1,71 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 22 Jun 2016 14:36:13 +0200
-Description: vcflib needs to be packaged separately
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -13,12 +13,9 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-
- SEQLIB_ROOT=../SeqLib
--VCFLIB_ROOT=../vcflib
--TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
--HTSLIB_ROOT=$(TABIX_ROOT)/htslib
-
--LIBS = -lbamtools -ltabixpp -lz -lm -lpthread
--INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
-+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
-+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
-
- all: autoversion ../bin/freebayes ../bin/bamleftalign
-
-@@ -66,14 +63,6 @@ OBJECTS=BedReader.o \
- Contamination.o \
- NonCall.o \
- SegfaultHandler.o \
-- ../vcflib/tabixpp/tabix.o \
-- ../vcflib/tabixpp/htslib/bgzf.o \
-- ../vcflib/smithwaterman/SmithWatermanGotoh.o \
-- ../vcflib/smithwaterman/disorder.cpp \
-- ../vcflib/smithwaterman/LeftAlign.o \
-- ../vcflib/smithwaterman/Repeats.o \
-- ../vcflib/smithwaterman/IndelAllele.o \
-- Variant.o \
- $(SEQLIB_ROOT)/src/libseqlib.a \
- $(SEQLIB_ROOT)/bwa/libbwa.a \
- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
-@@ -185,18 +174,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $
- IndelAllele.o: IndelAllele.cpp IndelAllele.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp
-
--Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp
-- $(CXX) $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
--
--../vcflib/tabixpp/tabix.o:
-- cd $(TABIX_ROOT)/ && make
--../vcflib/tabixpp/htslib/bgzf.o: ../vcflib/tabixpp/htslib/bgzf.c ../vcflib/tabixpp/htslib/htslib/bgzf.h
-- cd ../vcflib/tabixpp && $(MAKE)
--
--../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp
-- cd ../vcflib/smithwaterman && $(MAKE)
--
--
- VERSION_FILE=./version_git.h
- RELEASED_VERSION_FILE=./version_release.txt
-
-@@ -269,6 +246,5 @@ autoversion:
-
-
- clean:
-- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
-- cd ../vcflib/smithwaterman && make clean
-+ rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,4 +1,4 @@
--all: vcflib/Makefile log
-+all:
- cd src && $(MAKE)
-
- log: src/version_git.h
View it on GitLab: https://salsa.debian.org/med-team/freebayes/commit/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6
--
View it on GitLab: https://salsa.debian.org/med-team/freebayes/commit/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6
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