Author: Tim Booth <tbooth@ceh.ac.uk>
Last-Update: Wed, 01 Jan 2014 19:04:47 +0100 (by Andreas Tille)
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)