[med-svn] [bitseq] 03/14: Update patch to use Debian packaged samtools

[Andreas Tille]

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tille pushed a commit to branch master
in repository bitseq.

commit 269ca734cd4e904fad458d5a5381476f21fea867
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 1 18:20:56 2014 +0000

    Update patch to use Debian packaged samtools
---
 debian/patches/link_against_system_samtools | 52 ++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 15 deletions(-)

diff --git a/debian/patches/link_against_system_samtools b/debian/patches/link_against_system_samtools
index 6a55aba..5c6d282 100644
--- a/debian/patches/link_against_system_samtools
+++ b/debian/patches/link_against_system_samtools
@@ -1,5 +1,9 @@
---- a/ReadDistribution.h
-+++ b/ReadDistribution.h
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Wed, 01 Jan 2014 19:04:47 +0100 (by Andreas Tille)
+Description: link against Debian packaged samtools
+
+--- BitSeq-0.7.0.orig/ReadDistribution.h
++++ BitSeq-0.7.0/ReadDistribution.h
 @@ -21,8 +21,8 @@
  
  #else
@@ -11,19 +15,37 @@
  
  //#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
  /*
---- a/Makefile
-+++ b/Makefile
-@@ -25,11 +25,8 @@
- getWithinGeneExpression: getWithinGeneExpression.cpp common.o ArgumentParser.o TranscriptInfo.o PosteriorSamples.o common.h
- 	$(CXX) $(CXXFLAGS) getWithinGeneExpression.cpp common.o ArgumentParser.o TranscriptInfo.o PosteriorSamples.o -o getWithinGeneExpression
- 
--parseAlignment: parseAlignment.cpp common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o samtools/sam.o
--	$(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools samtools/*.o common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o parseAlignment.cpp -lz -o parseAlignment
--
+--- BitSeq-0.7.0.orig/Makefile
++++ BitSeq-0.7.0/Makefile
+@@ -63,8 +63,8 @@
+ getWithinGeneExpression: getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o
+ 	$(CXX) $(CXXFLAGS) $(LDFLAGS) getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression
+ 
+-parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/sam.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
+-	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread -Isamtools parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/*.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -o parseAlignment
++parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
++	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -lbam -o parseAlignment
+ 
+ transposeLargeFile: transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o
+ 	$(CXX) $(CXXFLAGS) $(LDFLAGS) transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o -o transposeLargeFile
+@@ -92,7 +92,7 @@
+ 	$(CXX) $(CXXFLAGS) -ffunction-sections -fdata-sections -c PosteriorSamples.cpp
+ 
+ ReadDistribution.o: ReadDistribution.cpp ReadDistribution.h TranscriptExpression.h TranscriptInfo.h TranscriptSequence.h 
+-	$(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools -c ReadDistribution.cpp
++	$(CXX) $(CXXFLAGS) $(OPENMP) -c ReadDistribution.cpp
+ 
+ Sampler.o: Sampler.cpp Sampler.h GibbsParameters.h
+ 	$(CXX) $(CXXFLAGS) $(BOOSTFLAGS) -c Sampler.cpp
+@@ -116,10 +116,7 @@
+ asa103/asa103.o:
+ 	make --directory asa103
+ 
 -samtools/sam.o:
 -	make --directory samtools
-+parseAlignment: parseAlignment.cpp common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o
-+	$(CXX) $(CXXFLAGS) $(OPENMP) common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o parseAlignment.cpp -lbam -lz -o parseAlignment
+-
+ # CLEAN:
+ clean:
+-	rm asa103/*.o samtools/*.o *.o $(PROGRAMS)
++	rm -f asa103/*.o samtools/*.o *.o $(PROGRAMS)
  
- convertSamples: convertSamples.cpp common.o ArgumentParser.o TranscriptInfo.o
- 	$(CXX) $(CXXFLAGS) convertSamples.cpp common.o ArgumentParser.o  TranscriptInfo.o -o convertSamples

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