query.end - query.start));
bis.close();
SAMIterator it = new SAMIterator(is, refFile);
is.seek(entries.get(0).containerStartOffset);
BAMQueryFilteringIterator bit = new BAMQueryFilteringIterator(
it, query.sequence, query.start, query.end,
BAMQueryFilteringIterator.QueryType.CONTAINED,
reader.getFileHeader());
source.it = bit;