From: Bo Li <bli@cs.wisc.edu>
Date: Thu, 25 Aug 2011 14:35:18 +0000 (-0500)
Subject: rsem v1.1.11, allow spaces appear in field seqname and attributes gene_id, transcript... 
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=90df7a1408511063de96e29658ffa289d43cc0bb

rsem v1.1.11, allow spaces appear in field seqname and attributes gene_id, transcript_id in GTF files
---

diff --git a/BamWriter.h b/BamWriter.h
index fd0b8b7..b39400f 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -479,7 +479,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper, Transcripts& transcripts)
 	bam_destroy1(b);
 	bam_destroy1(b2);
 
-	if (verbose) { printf("Bam output file is generated!"); }
+	if (verbose) { printf("Bam output file is generated!\n"); }
 }
 
 void BamWriter::tr2chr(const Transcript& transcript, int sp, int ep, int& pos, int& n_cigar, std::vector<uint8_t>& data) {
diff --git a/Transcript.h b/Transcript.h
index 8d7be7a..90f6e67 100644
--- a/Transcript.h
+++ b/Transcript.h
@@ -113,7 +113,10 @@ void Transcript::read(std::ifstream& fin) {
 	int s;
 	std::string tmp;
 
-	fin>>transcript_id>>gene_id>>seqname>>tmp>>length;
+	getline(fin, transcript_id);
+	getline(fin, gene_id);
+	getline(fin, seqname);
+	fin>>tmp>>length;
 	assert(tmp.length() == 1 && (tmp[0] == '+' || tmp[0] == '-'));
 	strand = tmp[0];
 	structure.clear();
@@ -130,7 +133,10 @@ void Transcript::read(std::ifstream& fin) {
 void Transcript::write(std::ofstream& fout) {
 	int s = structure.size();
 
-	fout<<transcript_id<<" "<<gene_id<<" "<<seqname<<" "<<strand<<" "<<length<<" ";
+	fout<<transcript_id<<std::endl;
+	fout<<gene_id<<std::endl;
+	fout<<seqname<<std::endl;
+	fout<<strand<<" "<<length<<std::endl;
 	fout<<s;
 	for (int i = 0; i < s; i++) fout<<" "<<structure[i].start<<" "<<structure[i].end;
 	fout<<std::endl;