[med-svn] [bitseq] 01/02: Update patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository bitseq.

commit 08ec95f6afdc658d50573b9b88883eac46cee125
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 2 09:54:46 2017 +0100

    Update patches
---
 debian/patches/hardening.patch                    | 14 ++++----
 debian/patches/link_against_system_samtools.patch | 41 +++++------------------
 2 files changed, 17 insertions(+), 38 deletions(-)

diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index cf2d122..2569bc2 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -2,15 +2,17 @@ Author: Andreas Tille <tille at debian.org>
 Last-Change: Wed, 01 Jan 2014 19:04:47 +0100
 Description: Propagate hardening options
 
---- BitSeq-0.7.0.orig/Makefile
-+++ BitSeq-0.7.0/Makefile
-@@ -6,8 +6,8 @@
- 
- 
+--- a/Makefile
++++ b/Makefile
+@@ -8,10 +8,10 @@ VERSION = 0.7.5
+ # Use O1 for debuiggging so it's not totally slow.
+ DBGFLAGS = -O1 -ggdb -U_FORTIFY_SOURCE
  COFLAGS = $(ARCH) -O2 -pipe
 -CXXFLAGS = -DBS_VERSION=\"$(VERSION)\" -Wall $(COFLAGS)
--LDFLAGS = -Wl,-gc-sections
 +CXXFLAGS += -DBS_VERSION=\"$(VERSION)\" -Wall $(COFLAGS)
+ # -Wvla does not work with old gcc
+ # -ffast-math segfaults with old gcc, don't use.
+-LDFLAGS = -Wl,-gc-sections
 +LDFLAGS += -Wl,-gc-sections
  BOOSTFLAGS = -I .
  OPENMP = -fopenmp -DSUPPORT_OPENMP
diff --git a/debian/patches/link_against_system_samtools.patch b/debian/patches/link_against_system_samtools.patch
index 5c6d282..de5cce8 100644
--- a/debian/patches/link_against_system_samtools.patch
+++ b/debian/patches/link_against_system_samtools.patch
@@ -2,50 +2,27 @@ 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
- 
--#include "bam.h"
--#include "sam.h"
-+#include <samtools/bam.h>
-+#include <samtools/sam.h>
- 
- //#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
- /*
---- BitSeq-0.7.0.orig/Makefile
-+++ BitSeq-0.7.0/Makefile
-@@ -63,8 +63,8 @@
+--- a/Makefile
++++ b/Makefile
+@@ -67,8 +67,8 @@ getVariance: getVariance.cpp $(COMMON_DE
  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
+-	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread 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
+@@ -116,10 +116,6 @@ TranscriptInfo.o: TranscriptInfo.cpp Tra
+ TranscriptSequence.o: TranscriptSequence.cpp TranscriptSequence.h
+ transposeFiles.o: transposeFiles.cpp transposeFiles.h FileHeader.h
  
+-# EXTERNAL LIBRARIES:
 -samtools/sam.o:
 -	make --directory samtools
 -
  # CLEAN:
  clean:
--	rm asa103/*.o samtools/*.o *.o $(PROGRAMS)
-+	rm -f asa103/*.o samtools/*.o *.o $(PROGRAMS)
- 
+ 	rm *.o $(PROGRAMS)

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