Examples of htsjdk.samtools.filter.SamRecordFilter

            final Map<SAMReadGroupRecord, FastqQualityFormat> readGroupToFormat = new HashMap<SAMReadGroupRecord, FastqQualityFormat>();


            // Figure out the quality score encoding scheme for each read group.
            for (final SAMReadGroupRecord rg : inHeader.getReadGroups()) {
                final SamReader reader =  SamReaderFactory.makeDefault().validationStringency(VALIDATION_STRINGENCY).open(INPUT);
                final SamRecordFilter filter = new SamRecordFilter() {
                    public boolean filterOut(final SAMRecord rec) {
                        return !rec.getReadGroup().getId().equals(rg.getId());
                    }
                    public boolean filterOut(final SAMRecord first, final SAMRecord second) {
                        throw new UnsupportedOperationException();

     */
    MultiHitAlignedReadIterator(final CloseableIterator<SAMRecord> querynameOrderIterator,
                                final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy) {
        this.primaryAlignmentSelectionStrategy = primaryAlignmentSelectionStrategy;
        peekIterator = new PeekableIterator<SAMRecord>(new FilteringIterator(querynameOrderIterator,
                new SamRecordFilter() {
                    // Filter unmapped reads.
                    public boolean filterOut(final SAMRecord record) {
                        return record.getReadUnmappedFlag() || SAMUtils.cigarMapsNoBasesToRef(record.getCigar());
                    }
                    public boolean filterOut(final SAMRecord first, final SAMRecord second) {

Related Classes of htsjdk.samtools.filter.SamRecordFilter

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