Fixed a bug to make RSEM generated BAM file valid input for RSEM

diff --git a/BamWriter.h b/BamWriter.h
index bbdd2983490fc147ab64e1a26106922ba170d077..8c568f348f361fd009c964cd2b9ad021e50fc257 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -173,33 +173,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 }
 
 void BamWriter::convert(bam1_t *b, double prb) {
-       const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
-
-       int pos = b->core.pos;
-       int readlen = b->core.l_qseq;
-
-       std::vector<uint32_t> data;
-       data.clear();
-
-       int core_pos, core_n_cigar;
-       std::vector<Interval> vec;
-       vec.assign(1, Interval(1, transcript.getLength()));
-       // make an artificial chromosome coordinates for the transcript to get new CIGAR strings
-       tr2chr(Transcript("", "", "", '+', vec, ""), pos + 1, pos + readlen, core_pos, core_n_cigar, data);
-       assert(core_pos >= 0);
-
-       int rest_len = b->data_len - b->core.l_qname - b->core.n_cigar * 4;
-       b->data_len = b->core.l_qname + core_n_cigar * 4 + rest_len;
-       expand_data_size(b);
-       uint8_t* pt = b->data + b->core.l_qname;
-       memmove(pt + core_n_cigar * 4, pt + b->core.n_cigar * 4, rest_len);
-       for (int i = 0; i < core_n_cigar; i++) { memmove(pt, &data[i], 4); pt += 4; }
-
-       b->core.pos = core_pos;
-       b->core.n_cigar = core_n_cigar;
        b->core.qual = getMAPQ(prb);
-       b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&(b->core), bam1_cigar(b)));
-
        float val = (float)prb;
        bam_aux_append(b, "ZW", 'f', bam_aux_type2size('f'), (uint8_t*)&val);
 }

diff --git a/README.md b/README.md
index 8ce3d3897062541a335c291ef9c6dfed89e833f4..1e64574d8683f73779cad2bc95a32eb9001c1d52 100644 (file)
--- a/README.md
+++ b/README.md
@@ -174,7 +174,7 @@ Here are some guidance for visualizing transcript coordinate files using IGV:
 
 1) Import the transcript sequences as a genome 
 
-Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.transcripts.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
+Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.idx.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
 
 2) Load visualization files