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Author: Tim Booth <tbooth@ceh.ac.uk>
Last-Update: 2014-01-01
Reviewed-By: Andreas Tille <tille@debian.org>
Description: link against Debian packaged samtools
--- 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 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 -lbam -lz -o parseAlignment
transposeLargeFile: transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o
$(CXX) $(CXXFLAGS) $(LDFLAGS) transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o -o transposeLargeFile
@@ -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 *.o $(PROGRAMS)
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