mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
-
mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ // TODO JAL-1887 should be fixed from here
mappingDetails.append(
String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
.append(" ");