Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM...

[rsem.git] / makefile

diff --git a/makefile b/makefile
index 44d73696f1ddf63c1b09732ef84b052909ff539b..900a8b3d3a7d47db5cc29ada4e1c78fb08d38b64 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,7 +1,7 @@
 CC = g++
 CFLAGS = -Wall -c -I.
 COFLAGS = -Wall -O3 -ffast-math -c -I.
-PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator
+PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 
 
 all : $(PROGRAMS)
@@ -133,6 +133,9 @@ rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
 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