* (snp) queue is the same. Also make sure that the context is in the order
* specified by the input files.
*/
private void validateSnpAndIndelResults(final File output, final Queue<String> indelContigPositions, final Queue<String> snpContigPositions) {
final VCFFileReader outputReader = new VCFFileReader(output, false);
final VariantContextComparator outputComparator = outputReader.getFileHeader().getVCFRecordComparator();
VariantContext last = null;
final CloseableIterator<VariantContext> iterator = outputReader.iterator();
while (iterator.hasNext()) {
final VariantContext outputContext = iterator.next();
if (outputContext.isIndel()) Assert.assertEquals(getContigPosition(outputContext), indelContigPositions.poll());
if (outputContext.isSNP()) Assert.assertEquals(getContigPosition(outputContext), snpContigPositions.poll());
if (last != null) Assert.assertTrue(outputComparator.compare(last, outputContext) <= 0);
last = outputContext;
}
iterator.close();
// We should have polled everything off the indel (snp) queues