private int compareCoordinates(final SAMRecord record1, final SAMRecord record2) {
final int seqIndex1 = record1.getReferenceIndex();
final int seqIndex2 = record2.getReferenceIndex();
if (seqIndex1 == -1) {
return ((seqIndex2 == -1) ? 0 : -1);
} else if (seqIndex2 == -1) {
return 1;
}
int result = seqIndex1 - seqIndex2;
if (result != 0) {
return result;
}
result = record1.getAlignmentStart() - record2.getAlignmentStart();
return result;
}
private boolean passesFilter(
final SAMRecord record,
final String sequence,
final int startPos,
final int endPos,
final boolean contained) {
if (record == null) {
return false;
}
if (!safeEquals(record.getReferenceName(), sequence)) {
return false;
}
final int alignmentStart = record.getAlignmentStart();
int alignmentEnd = record.getAlignmentEnd();
if (alignmentStart <= 0) {
assertTrue(record.getReadUnmappedFlag());
return false;
}
if (alignmentEnd <= 0) {
// For indexing-only records, treat as single base alignment.
assertTrue(record.getReadUnmappedFlag());
alignmentEnd = alignmentStart;
}
if (contained) {
if (startPos != 0 && alignmentStart < startPos) {
return false;
}
if (endPos != 0 && alignmentEnd > endPos) {
return false;
}
} else {
if (startPos != 0 && alignmentEnd < startPos) {
return false;
}
if (endPos != 0 && alignmentStart > endPos) {
return false;
}
}
return true;
}