Examples of AlignedFilter

Examples of htsjdk.samtools.filter.AlignedFilter

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            if (WRITE_READS_FILES) writeReadsFile(INPUT);

            switch (FILTER) {
                case includeAligned:
                    filterReads(new FilteringIterator(new SAMFileReader(INPUT).iterator(),
                    new AlignedFilter(true), true));
                    break;
                case excludeAligned:
                    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;
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