fixed a bug for transcript set as reference

diff --git a/BamWriter.h b/BamWriter.h
index 7f3c562309678389e6f98aae29addce776110939..e33a07fdc35e335aaf2cfe10d900fca0efd1eee2 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -174,6 +174,7 @@ BamWriter::BamWriter(char inpType, const char* inpF, const char* fn_list, const
                }
        }
 
+
        out = samopen(outF, "wb", out_header);
        assert(out != 0);
 

diff --git a/synthesisRef.cpp b/synthesisRef.cpp
index 005cf95fee33e1031077a5993b1c771f1e4d6579..3bb28086b3fee8755d81b88ad8f053b1ffd5a0af 100644 (file)
--- a/synthesisRef.cpp
+++ b/synthesisRef.cpp
@@ -18,7 +18,7 @@ map<string, string> name2seq;
 map<string, string>::iterator iter;
 
 Transcripts transcripts;
-char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN];
+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();
@@ -90,9 +91,16 @@ 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[]) {