Fixed a minor bug which only affects paired-end reads for reporting how many alignmen...

[rsem.git] / synthesisRef.cpp

diff --git a/synthesisRef.cpp b/synthesisRef.cpp
index 005cf95fee33e1031077a5993b1c771f1e4d6579..8ce268c197dfff87b7c6d989077fe863cc0d1a4c 100644 (file)
--- a/synthesisRef.cpp
+++ b/synthesisRef.cpp
@@ -17,8 +17,8 @@ int M;
 map<string, string> name2seq;
 map<string, string>::iterator iter;
 
-Transcripts transcripts;
-char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN];
+Transcripts transcripts(1); // no genome, just transcript set
+char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN], chromListF[STRLEN];
 
 bool hasMappingFile;
 char mappingFile[STRLEN];
@@ -56,12 +56,13 @@ char check(char c) {
 }
 
 void writeResults(char* refName) {
-       ofstream fout;
+       ofstream fout, fout2;
        string cur_gene_id, name;
 
        sprintf(groupF, "%s.grp", refName);
        sprintf(tiF, "%s.ti", refName);
        sprintf(refFastaF, "%s.transcripts.fa", refName);
+       sprintf(chromListF, "%s.chrlist", refName);
 
        transcripts.writeTo(tiF);
        if (verbose) { printf("Transcript Information File is generated!\n"); }
@@ -79,7 +80,7 @@ void writeResults(char* refName) {
        fout.close();
        if (verbose) { printf("Group File is generated!\n"); }
 
-       // We have to generate this .transcripts.fa, even reference_file is only one. Reason : polyA choice 2, need ">transcript_id"
+       fout2.open(chromListF);
        fout.open(refFastaF);
        for (int i = 1; i <= M; i++) {
                name = transcripts.getTranscriptAt(i).getTranscriptID();
@@ -90,13 +91,20 @@ void writeResults(char* refName) {
                }
                fout<<">"<<name<<endl;
                fout<<iter->second<<endl;
+
+               fout2<<name<<'\t'<<iter->second.length()<<endl;
        }
        fout.close();
-       if (verbose) { printf("Extracted Sequences File is generated!\n"); }
+       fout2.close();
+       
+       if (verbose) { 
+         printf("Chromosome List File is generated!\n"); 
+         printf("Extracted Sequences File is generated!\n"); 
+       }
 }
 
 int main(int argc, char* argv[]) {
-       if (argc < 5 || (hasMappingFile = atoi(argv[3])) && argc < 6) {
+  if (argc < 5 || ((hasMappingFile = atoi(argv[3])) && argc < 6)) {
                printf("Usage: synthesisRef refName quiet hasMappingFile [mappingFile] reference_file_1 [reference_file_2 ...]\n");
                exit(-1);
        }