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 void checkPassesFilter(
final boolean expected,
final SAMRecord record,
final String sequence,
final int startPos,
final int endPos,
final boolean contained) {
final boolean passes = passesFilter(record, sequence, startPos, endPos, contained);
if (passes != expected) {
System.out.println(
"Error: Record erroneously " + (passes ? "passed" : "failed") + " filter.");
System.out.println(" Record: " + record.getSAMString());
System.out.println(
" Filter: "
+ sequence
+ ":"
+ startPos
+ "-"
+ endPos
+ " ("
+ (contained ? "contained" : "overlapping")
+ ")");
assertEquals(passes, expected);
}
}
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;
}
private int runQueryTest(
final URL bamURL,
final String sequence,
final int startPos,
final int endPos,
final boolean contained) {
verbose("Testing query " + sequence + ":" + startPos + "-" + endPos + " ...");
final SamReader reader1 =
SamReaderFactory.makeDefault()
.disable(SamReaderFactory.Option.EAGERLY_DECODE)
.open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE));
final SamReader reader2 =
SamReaderFactory.makeDefault()
.disable(SamReaderFactory.Option.EAGERLY_DECODE)
.open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE));
final Iterator<SAMRecord> iter1 = reader1.query(sequence, startPos, endPos, contained);
final Iterator<SAMRecord> iter2 = reader2.iterator();
// Compare ordered iterators.
// Confirm that iter1 is a subset of iter2 that properly filters.
SAMRecord record1 = null;
SAMRecord record2 = null;
int count1 = 0;
int count2 = 0;
int beforeCount = 0;
int afterCount = 0;
while (true) {
if (record1 == null && iter1.hasNext()) {
record1 = iter1.next();
count1++;
}
if (record2 == null && iter2.hasNext()) {
record2 = iter2.next();
count2++;
}
// System.out.println("Iteration:");
// System.out.println(" Record1 = " + ((record1 == null) ? "null" : record1.format()));
// System.out.println(" Record2 = " + ((record2 == null) ? "null" : record2.format()));
if (record1 == null && record2 == null) {
break;
}
if (record1 == null) {
checkPassesFilter(false, record2, sequence, startPos, endPos, contained);
record2 = null;
afterCount++;
continue;
}
assertNotNull(record2);
final int ordering = compareCoordinates(record1, record2);
if (ordering > 0) {
checkPassesFilter(false, record2, sequence, startPos, endPos, contained);
record2 = null;
beforeCount++;
continue;
}
assertTrue(ordering == 0);
checkPassesFilter(true, record1, sequence, startPos, endPos, contained);
checkPassesFilter(true, record2, sequence, startPos, endPos, contained);
assertEquals(record1.getReadName(), record2.getReadName());
assertEquals(record1.getReadString(), record2.getReadString());
record1 = null;
record2 = null;
}
CloserUtil.close(reader1);
CloserUtil.close(reader2);
verbose("Checked " + count1 + " records against " + count2 + " records.");
verbose("Found " + (count2 - beforeCount - afterCount) + " records matching.");
verbose("Found " + beforeCount + " records before.");
verbose("Found " + afterCount + " records after.");
return count1;
}
