}
iterator.setEmitUncoveredLoci(false);
iterator.setMappingQualityScoreCutoff(MINIMUM_MAPPING_QUALITY);
iterator.setSamFilters(Arrays.asList(
new NotPrimaryAlignmentFilter(),
new DuplicateReadFilter(),
new InsertSizeFilter(MINIMUM_INSERT_SIZE, MAXIMUM_INSERT_SIZE)
));
log.info("Starting iteration.");
long nextLogTime = 0;