Examples of htsjdk.samtools.filter.FilteringIterator

htsjdk.samtools.filter.FilteringIterator


        int aligned = 0;
        int unmapped = 0;


        // Get the aligned records and set up the first one
        alignedIterator = new MultiHitAlignedReadIterator(new FilteringIterator(getQuerynameSortedAlignedRecords(), alignmentFilter), primaryAlignmentSelectionStrategy);
        HitsForInsert nextAligned = nextAligned();


        // Create the sorting collection that will write the records in the coordinate order
        // to the final bam file
        final SortingCollection<SAMRecord> sorted = SortingCollection.newInstance(

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                    }
                    public boolean filterOut(final SAMRecord first, final SAMRecord second) {
                        throw new UnsupportedOperationException();
                    }
                };
                readGroupToFormat.put(rg, QualityEncodingDetector.detect(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, new FilteringIterator(reader.iterator(), filter), RESTORE_ORIGINAL_QUALITIES));
                CloserUtil.close(reader);
            }
            for(final SAMReadGroupRecord r : readGroupToFormat.keySet()) {
                log.info("Detected quality format for " + r.getReadGroupId() + ": " + readGroupToFormat.get(r));
            }

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        int fileIndex = 0;
        initializeNextBfqFiles(fileIndex++);


        int records = 0;


        final FilteringIterator it = new FilteringIterator(iterator, new AggregateFilter(filters));
        while (it.hasNext()) {
            final SAMRecord record = it.next();
            records++;
            if (records % increment == 0) {


                record.setReadName(record.getReadName() + "/1");
                writeFastqRecord(codec1, record);

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            final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
            filters.add(new TagFilter(ReservedTagConstants.XN, 1));
            if (!this.includeNonPfReads) {
                filters.add(new FailsVendorReadQualityFilter());
            }
            final FilteringIterator itr = new FilteringIterator(it, new AggregateFilter(filters));
            while (itr.hasNext()) {
                itr.next();
                count++;
            }
        }
        else {
            while (it.hasNext()) {

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            IOUtil.assertFileIsWritable(OUTPUT);
            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;
                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!");
            }

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     *                                          the input what should be primary.
     */
    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());
                    }

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Related Classes of htsjdk.samtools.filter.FilteringIterator

picard.fastq.BamToBfqWriter

picard.sam.AbstractAlignmentMerger

picard.sam.FilterSamReads

picard.sam.MultiHitAlignedReadIterator

picard.sam.RevertSam

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