filters.add(new NotPrimaryAlignmentFilter()); if (!INCLUDE_DUPLICATES) filters.add(new DuplicateReadFilter()); filters.add(new AlignedFilter(true)); // discard unmapped reads
filters.add(new NotPrimaryAlignmentFilter()); if (!INCLUDE_DUPLICATES) filters.add(new DuplicateReadFilter()); filters.add(new AlignedFilter(true)); // discard unmapped reads
filters.add(new NotPrimaryAlignmentFilter()); filters.add(new DuplicateReadFilter()); if (MINIMUM_INSERT_SIZE > 0 || MAXIMUM_INSERT_SIZE > 0) {
filters.add(new NotPrimaryAlignmentFilter()); filters.add(new DuplicateReadFilter()); if (MINIMUM_INSERT_SIZE > 0 || MAXIMUM_INSERT_SIZE > 0) {