X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=Transcript.h;h=f7afa2b20542ebdb2f4883d1cc12631eb2b1176e;hp=8d7be7ae68afae09c773144e45db4ba79b81b36f;hb=92b24279a3ecc72946e7e7c23149ad0d181f373a;hpb=37513308b7557ae65899e59df8e43b5dec90da5c

diff --git a/Transcript.h b/Transcript.h
index 8d7be7a..f7afa2b 100644
--- a/Transcript.h
+++ b/Transcript.h
@@ -10,6 +10,10 @@
 
 #include "utils.h"
 
+/**
+   If no genome is provided, seqname field is used to store the allele name.
+ */
+
 struct Interval {
 	int start, end;
 
@@ -49,7 +53,7 @@ public:
 	}
 
 	bool operator< (const Transcript& o) const {
-	  return gene_id < o.gene_id || (gene_id == o.gene_id && transcript_id < o.transcript_id);
+	  return gene_id < o.gene_id || (gene_id == o.gene_id && transcript_id < o.transcript_id) || (gene_id == o.gene_id && transcript_id == o.transcript_id && seqname < o.seqname);
 	}
 
 	const std::string& getTranscriptID() const { return transcript_id; }
@@ -113,7 +117,10 @@ 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 +137,10 @@ 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;