Fixed a problem that will lead compilation errors for Mac OS

diff --git a/extractRef.cpp b/extractRef.cpp
index fb7d3ecb586d36e586d8698a9f4c94bc0ec4cc46..2a26bce4a9970056f997a2015d951fa5c239be06 100644 (file)
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -303,8 +303,9 @@ int main(int argc, char* argv[]) {
        for (int i = 1; i <= M; i++) {
                if (seqs[i] == "") {
                        const Transcript& transcript = transcripts.getTranscriptAt(i);
-                       fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s, whose information might not be provided! Please check if the chromosome directory is set correctly or the list of chromosome files is complete.\n", \
-                                       transcript.getTranscriptID().c_str(), transcript.getSeqName().c_str());
+
+                       fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s! Loading chromosome %s's sequence is failed. Please check if 1) the chromosome directory is set correctly; 2) the list of chromosome files is complete; 3) the FASTA files containing chromosome sequences are not truncated or having wrong format.\n", \
+                               transcript.getTranscriptID().c_str(), transcript.getSeqName().c_str(), transcript.getSeqName().c_str());
                        exit(-1);
                }
        }

diff --git a/makefile b/makefile
index 3c48e69e91f6dbefee50b52d5d3a14b08dcac4ec..c95fd14467cb0263ac6122d321cd7af4f8e0b9bb 100644 (file)
--- a/makefile
+++ b/makefile
@@ -50,7 +50,7 @@ SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h
 
 
 rsem-parse-alignments : parseIt.o sam/libbam.a
-       $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
+       $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread 
 
 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) -Wall -O2 -c -I. parseIt.cpp
@@ -93,13 +93,13 @@ bc_aux.h : sam/bam.h
 BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
 
 rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
-       $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -o $@
+       $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 
 rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
-       $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -o $@
+       $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 
 rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-       $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -o $@
+       $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 
 wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
        $(CC) $(COFLAGS) wiggle.cpp
@@ -127,13 +127,13 @@ calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h
        $(CC) $(COFLAGS) calcCI.cpp
 
 rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
-       $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -o $@
+       $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
 
 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 $@
+       $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -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 $@
+       $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 
 .PHONY: ebseq