final Iterator<SAMRecord> iterator = (new SAMFileReader(IOUtil.openFileForReading(this.bamFile))).iterator();
// Filter out noise reads and reads that fail the quality filter
final TagFilter tagFilter = new TagFilter(ReservedTagConstants.XN, 1);
final FailsVendorReadQualityFilter qualityFilter = new FailsVendorReadQualityFilter();
final WholeReadClippedFilter clippedFilter = new WholeReadClippedFilter();
if (!pairedReads) {
List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
filters.add(tagFilter);