From 6306c61d30a4e727027c26488272c9ff683f8236 Mon Sep 17 00:00:00 2001 From: Bo Li Date: Wed, 8 Jan 2014 18:56:45 -0600 Subject: [PATCH] Fixed a problem that will lead compilation errors for Mac OS --- extractRef.cpp | 5 +++-- makefile | 14 +++++++------- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/extractRef.cpp b/extractRef.cpp index fb7d3ec..2a26bce 100644 --- 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 3c48e69..c95fd14 100644 --- 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 -- 2.39.2