From: Bo Li <bli@cs.wisc.edu>
Date: Sun, 11 Mar 2012 10:47:20 +0000 (-0500)
Subject: Modified makefile to work for gcc version 4.5.3 or higher
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=f67ec16ff8add74c17df026f77cf39e5a1aca051

Modified makefile to work for gcc version 4.5.3 or higher
---

diff --git a/README.md b/README.md
index 836a367..6e8acd8 100644
--- a/README.md
+++ b/README.md
@@ -121,7 +121,7 @@ If your file does not satisfy the requirements, you can use
 '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
diff --git a/makefile b/makefile
index 900a8b3..e2711b5 100644
--- a/makefile
+++ b/makefile
@@ -54,7 +54,7 @@ rsem-parse-alignments : parseIt.o sam/libbam.a
 	$(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
@@ -132,10 +132,10 @@ 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