[med-svn] [bitseq] 01/01: Link -lbam before -lz to fix build with -Wl, --as-needed

[Graham Inggs]

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ginggs pushed a commit to branch master
in repository bitseq.

commit ce48c26201f9548fb7bb42da0eab547e53db282b
Author: Graham Inggs <ginggs at debian.org>
Date:   Fri Feb 2 12:11:51 2018 +0200

    Link -lbam before -lz to fix build with -Wl,--as-needed
---
 debian/changelog                                  | 6 ++++++
 debian/patches/link_against_system_samtools.patch | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index f8ab7f8..fc88e74 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bitseq (0.7.5+dfsg-4) UNRELEASED; urgency=medium
+
+  * Link -lbam before -lz to fix build with -Wl,--as-needed
+
+ -- Graham Inggs <ginggs at debian.org>  Fri, 02 Feb 2018 09:30:20 +0000
+
 bitseq (0.7.5+dfsg-3) unstable; urgency=medium
 
   * Build-Depends: python-numpy (Thanks for the patch to Chris Lamb
diff --git a/debian/patches/link_against_system_samtools.patch b/debian/patches/link_against_system_samtools.patch
index de5cce8..4fa7739 100644
--- a/debian/patches/link_against_system_samtools.patch
+++ b/debian/patches/link_against_system_samtools.patch
@@ -11,7 +11,7 @@ Description: link against Debian packaged samtools
 -parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/sam.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
 -	$(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
++	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lbam -lz -o parseAlignment
  
  transposeLargeFile: transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o
  	$(CXX) $(CXXFLAGS) $(LDFLAGS) transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o -o transposeLargeFile

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