'convert-sam-for-rsem' to convert it into a BAM file which RSEM can
process. Please run
- convert-sam-for-rsem --help
+ convert-sam-for-rsem --help
to get usage information or visit the [convert-sam-for-rsem
documentation
$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz
parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
- $(CC) $(COFLAGS) parseIt.cpp
+ $(CC) -Wall -O2 -c -I. parseIt.cpp
rsem-build-read-index : utils.h buildReadIndex.cpp
rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -o $@
-
+
rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -o $@
-
+
clean:
rm -f *.o *~ $(PROGRAMS)
cd sam ; ${MAKE} clean