Examples of picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar @author Nils Homer

                    // When we hit the unmapped reads with no coordinate, no reason to continue.
                    break;
                }
                // If this read is unmapped but sorted with the mapped reads, just skip it.
            } else if (!rec.isSecondaryOrSupplementary()) {
                final ReadEndsForMarkDuplicates fragmentEnd = buildReadEnds(header, index, rec);
                this.fragSort.add(fragmentEnd);


                if (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag()) {
                    final String key = rec.getAttribute(ReservedTagConstants.READ_GROUP_ID) + ":" + rec.getReadName();
                    ReadEndsForMarkDuplicates pairedEnds = tmp.remove(rec.getReferenceIndex(), key);


                    // See if we've already seen the first end or not
                    if (pairedEnds == null) {
                        pairedEnds = buildReadEnds(header, index, rec);
                        tmp.put(pairedEnds.read2ReferenceIndex, key, pairedEnds);

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        this.fragSort.doneAdding();
    }


    /** Builds a read ends object that represents a single read. */
    private ReadEndsForMarkDuplicates buildReadEnds(final SAMFileHeader header, final long index, final SAMRecord rec) {
        final ReadEndsForMarkDuplicates ends = new ReadEndsForMarkDuplicates();
        ends.read1ReferenceIndex = rec.getReferenceIndex();
        ends.read1Coordinate = rec.getReadNegativeStrandFlag() ? rec.getUnclippedEnd() : rec.getUnclippedStart();
        ends.orientation = rec.getReadNegativeStrandFlag() ? ReadEnds.R : ReadEnds.F;
        ends.read1IndexInFile = index;
        ends.score = DuplicateScoringStrategy.computeDuplicateScore(rec, this.DUPLICATE_SCORING_STRATEGY);

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        final int maxInMemory = (int) Math.min((Runtime.getRuntime().maxMemory() * 0.25) / SortingLongCollection.SIZEOF,
                (double) (Integer.MAX_VALUE - 5));
        log.info("Will retain up to " + maxInMemory + " duplicate indices before spilling to disk.");
        this.duplicateIndexes = new SortingLongCollection(maxInMemory, TMP_DIR.toArray(new File[TMP_DIR.size()]));


        ReadEndsForMarkDuplicates firstOfNextChunk = null;
        final List<ReadEndsForMarkDuplicates> nextChunk = new ArrayList<ReadEndsForMarkDuplicates>(200);


        // First just do the pairs
        log.info("Traversing read pair information and detecting duplicates.");
        for (final ReadEndsForMarkDuplicates next : this.pairSort) {

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     *
     * @param list
     */
    private void markDuplicatePairs(final List<ReadEndsForMarkDuplicates> list) {
        short maxScore = 0;
        ReadEndsForMarkDuplicates best = null;


        /** All read ends should have orientation FF, FR, RF, or RR **/
        for (final ReadEndsForMarkDuplicates end : list) {
            if (end.score > maxScore || best == null) {
                maxScore = end.score;

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            for (final ReadEndsForMarkDuplicates end : list) {
                if (!end.isPaired()) addIndexAsDuplicate(end.read1IndexInFile);
            }
        } else {
            short maxScore = 0;
            ReadEndsForMarkDuplicates best = null;
            for (final ReadEndsForMarkDuplicates end : list) {
                if (end.score > maxScore || best == null) {
                    maxScore = end.score;
                    best = end;
                }

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Related Classes of picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

picard.sam.markduplicates.MarkDuplicates

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