[med-svn] [freebayes] 01/01: Fix patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository freebayes.

commit 83dbc9f4370f7e0526f237d2d42f6cf2fb6e5436
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 14:40:24 2016 +0200

    Fix patch
---
 debian/patches/series                           |  2 +-
 debian/patches/use_debian_packaged_vcflib.patch | 28 +++++++++++++------------
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/debian/patches/series b/debian/patches/series
index c24532e..84b151d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-use_debian_packaged_vcflib.patch
 use_debian_packaged_bamtools.patch
+use_debian_packaged_vcflib.patch
diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch
index b58ee7d..5c91761 100644
--- a/debian/patches/use_debian_packaged_vcflib.patch
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -4,18 +4,20 @@ Description: vcflib needs to be packaged separately
 
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -15,8 +15,8 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
- BAMTOOLS_ROOT=../bamtools
- VCFLIB_ROOT=../vcflib
+@@ -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
  
--LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz -lm
--INCLUDE = -I$(BAMTOOLS_ROOT)/src -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
-+LIBS = -ltabix -lz -lm
-+INCLUDE = -I../ttmath
+-VCFLIB_ROOT=../vcflib
+-
+-LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabix -lz -lm
+-INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
++LIBS = -lbamtools -ltabix -lz -lm
++INCLUDE = -I/usr/include/bamtools -I../ttmath -I/usr/include/vcflib
  
  all: autoversion ../bin/freebayes ../bin/bamleftalign
  
-@@ -62,16 +62,7 @@ OBJECTS=BedReader.o \
+@@ -57,15 +55,7 @@ OBJECTS=BedReader.o \
  		Bias.o \
  		Contamination.o \
  		NonCall.o \
@@ -27,13 +29,12 @@ Description: vcflib needs to be packaged separately
 -		../vcflib/smithwaterman/LeftAlign.o \
 -		../vcflib/smithwaterman/Repeats.o \
 -		../vcflib/smithwaterman/IndelAllele.o \
--		Variant.o \
--		$(BAMTOOLS_ROOT)/lib/libbamtools.a
+-		Variant.o 
 +		SegfaultHandler.o
  
  HEADERS=multichoose.h version_git.h
  
-@@ -179,17 +170,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $
+@@ -173,17 +163,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp
  IndelAllele.o: IndelAllele.cpp IndelAllele.h
  	$(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp
  
@@ -51,9 +52,10 @@ Description: vcflib needs to be packaged separately
  VERSION_FILE=./version_git.h
  RELEASED_VERSION_FILE=./version_release.txt
  
-@@ -264,5 +244,4 @@ autoversion:
+@@ -257,5 +236,5 @@ autoversion:
+ 
  clean:
  	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
- 	test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean)
 -	cd ../vcflib/smithwaterman && make clean
++	# cd ../vcflib/smithwaterman && make clean
  

-- 
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