in = samopen(inpF, "rb", NULL);
assert(in != 0);
+ transcripts.buildMappings(in->header->n_targets, in->header->target_name);
+
bam_header_t *out_header = sam_header_read2(chr_list);
refmap.clear();
for (int i = 0; i < out_header->n_targets; i++) {
// at least one segment is not properly mapped
if ((b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004))) continue;
- const Transcript& transcript = transcripts.getTranscriptAt(b->core.tid + 1);
+ const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
convert(b, transcript);
if (isPaired) {