private void verifyRecord(final SAMRecord last, final SAMRecord cur) {
if (checkOrderP && isOutOfOrder(last, cur)) {
this.last = null;
throw new UserException.MissortedBAM(
String.format(
"reads are out of order:%nlast:%n%s%ncurrent:%n%s%n", last.format(), cur.format()));
}
}
private boolean isOutOfOrder(final SAMRecord last, final SAMRecord cur) {
if (last == null || cur.getReadUnmappedFlag()) return false;
else {
if (last.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
|| last.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
throw new UserException.MalformedBAM(
last, String.format("read %s has inconsistent mapping information.", last.format()));
if (cur.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
|| cur.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
throw new UserException.MalformedBAM(
last, String.format("read %s has inconsistent mapping information.", cur.format()));
return (last.getReferenceIndex() > cur.getReferenceIndex())
|| (last.getReferenceIndex().equals(cur.getReferenceIndex())
&& last.getAlignmentStart() > cur.getAlignmentStart());
}
}
