Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecordCoordinateComparator

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    private final class SplitReadComparator implements Comparator<SplitRead> {

        private final SAMRecordCoordinateComparator readComparator;

        public SplitReadComparator() {
            readComparator = new SAMRecordCoordinateComparator();
        }
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    private T walkOverPairs(ReadPairWalker<M,T> walker, Shard shard, List<SAMRecord> reads, T sum) {
        // update the number of reads we've seen
        shard.getReadMetrics().incrementNumIterations();

        // Sort the reads present in coordinate order.
        Collections.sort(reads,new SAMRecordCoordinateComparator());

        final boolean keepMeP = walker.filter(reads);
        if (keepMeP) {
            M x = walker.map(reads);
            sum = walker.reduce(x, sum);
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        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(
            SAMRecord.class, new BAMRecordCodec(header), new SAMRecordCoordinateComparator(),
            MAX_RECORDS_IN_RAM);

        while (unmappedIterator.hasNext()) {
            // Load next unaligned read or read pair.
            final SAMRecord rec = unmappedIterator.next();
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Related Classes of htsjdk.samtools.SAMRecordCoordinateComparator

  • org.broadinstitute.gatk.engine.traversals.TraverseReadPairs
  • org.broadinstitute.gatk.tools.walkers.rnaseq.OverhangFixingManager$SplitReadComparator
  • picard.sam.AbstractAlignmentMerger
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