filterReads(new FilteringIterator(new SAMFileReader(INPUT).iterator(),
new AlignedFilter(false), true));
break;
case includeReadList:
filterReads(new FilteringIterator(new SAMFileReader(INPUT).iterator(),
new ReadNameFilter(READ_LIST_FILE, true)));
break;
case excludeReadList:
filterReads(new FilteringIterator(new SAMFileReader(INPUT).iterator(),
new ReadNameFilter(READ_LIST_FILE, false)));
break;
default:
throw new UnsupportedOperationException(FILTER.name() + " has not been implemented!");
}