diff --git a/bwa-postalt.js b/bwa-postalt.js index 9abc674..6cf3dc7 100644 --- a/bwa-postalt.js +++ b/bwa-postalt.js @@ -582,7 +582,7 @@ function bwa_postalt(args) if (opt.verbose >= 5) print(obj2str(hits[i])); if (hits[i].g != reported_g || i == reported_i) continue; if (!opt.show_pri && idx_alt[hits[i].ctg] == null) continue; - var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0]; + var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, t[6], t[7], t[8]]; // print sequence/quality and set the rev flag if (hits[i].rev == hits[reported_i].rev) { s.push(t[9], t[10]);