private List<String> getReferenceNames(final URL bamFile) throws IOException {
final SamReader reader =
SamReaderFactory.makeDefault().open(SamInputResource.of(bamFile.openStream()));
final List<String> result = new ArrayList<String>();
final List<SAMSequenceRecord> seqRecords =
reader.getFileHeader().getSequenceDictionary().getSequences();
for (final SAMSequenceRecord seqRecord : seqRecords) {
if (seqRecord.getSequenceName() != null) {
result.add(seqRecord.getSequenceName());
}
}
reader.close();
return result;
}
private void runLocalRemoteTest(
final URL bamURL,
final File bamFile,
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(bamFile).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.query(sequence, startPos, endPos, contained);
final List<SAMRecord> records1 = new ArrayList<SAMRecord>();
final List<SAMRecord> records2 = new ArrayList<SAMRecord>();
while (iter1.hasNext()) {
records1.add(iter1.next());
}
while (iter2.hasNext()) {
records2.add(iter2.next());
}
assertTrue(records1.size() > 0);
assertEquals(records1.size(), records2.size());
for (int i = 0; i < records1.size(); i++) {
// System.out.println(records1.get(i).format());
assertEquals(records1.get(i).getSAMString(), records2.get(i).getSAMString());
}
}
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;
}