Refresh and restructure patches

Author: Andreas Tille <tille@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

Author: Fabian Klötzl <fabian@kloetzl.info>

Date: Mon, 4 Sep 2017 12:27:38 +0200

Acked-by: Andreas Tille <tille@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 << "]";

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

 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

Author: Andreas Tille <tille@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

Description: Use Debian packaged bamtools

--- a/src/Makefile

+++ b/src/Makefile

@@ -12,10 +12,8 @@ C=gcc

@@ -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 = -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`

-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

@@ -33,12 +31,6 @@ gprof:

@@ -45,12 +39,6 @@ gprof:

 .PHONY: all static debug profiling gprof

 OBJECTS=BedReader.o \

 		CNV.o \

 		fastlz.o \

@@ -62,11 +54,7 @@ OBJECTS=BedReader.o \

 		Bias.o \

@@ -75,17 +63,7 @@ OBJECTS=BedReader.o \

 		Contamination.o \

 		NonCall.o \

-		SegfaultHandler.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

+		SegfaultHandler.o

+		Variant.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)

@@ -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 $(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: $(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) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)

 	$(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)

-bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)

-bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)

+bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)

 	$(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)

 	$(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)

@@ -99,7 +87,7 @@ alleles.o: alleles.cpp AlleleParser.o Al

@@ -118,7 +96,7 @@ alleles.o: alleles.cpp AlleleParser.o Al

 dummy.o: dummy.cpp AlleleParser.o Allele.o

 	$(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp

 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp

-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a

-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a ../vcflib/tabixpp/tabix.o

+freebayes.o: freebayes.cpp TryCatch.h

 	$(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp

 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp

 fastlz.o: fastlz.c fastlz.h

@@ -120,7 +108,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle

@@ -139,7 +117,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle

 Ewens.o: Ewens.cpp Ewens.h

 	$(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp

 	$(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) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp

 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c AlleleParser.cpp

 Utility.o: Utility.cpp Utility.h Sum.h Product.h

@@ -168,7 +156,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli

@@ -187,22 +165,12 @@ bamleftalign.o: bamleftalign.cpp LeftAli

 bamfiltertech.o: bamfiltertech.cpp

 	$(CXX) $(CFLAGS) $(INCLUDE) -c 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) $(CFLAGS) $(INCLUDE) -c 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