Examples of org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState

org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState

Iterator that traverses a SAM File, accumulating information on a per-locus basis Produces AlignmentContext objects, that contain ReadBackedPileups of PileupElements. This class has its core job of converting an iterator of ordered SAMRecords into those RBPs. There are a few constraints on required and ensured by LIBS: -- Requires the Iterator to returns reads in coordinate sorted order, consistent with the ordering defined by the SAM file format. That that for performance reasons this constraint isn't actually enforced. The behavior of LIBS is undefined in the case where the reads are badly ordered. -- The reads in the ReadBackedPileup are themselves in the order of appearance of the reads from the iterator. That is, the pileup is ordered in a way consistent with the SAM coordinate ordering -- Only aligned reads with at least one on-genomic cigar operator are passed on in the pileups. That is, unmapped reads or reads that are all insertions (10I) or soft clipped (10S) are not passed on. -- LIBS can perform per-sample downsampling of a variety of kinds. -- Because of downsampling there's no guarantee that: -- A read that could be aligned to a position will actually occur in the pileup (downsampled away) -- A read that appears in a previous pileup that could align to a future position will actually occur in that pileup. That is, a read might show up at position i but be downsampled away in the pileup at j -- LIBS can optionally capture all of the reads that come off the iterator, before any leveling downsampling occurs, if requested. This allows users of LIBS to see both a ReadBackedPileup view of the data as well as a stream of unique, sorted reads


        if ( debuggingWriter != null )
            for ( final GATKSAMRecord read : reads )
                debuggingWriter.addAlignment(read);


        final LocusIteratorByState libs = new LocusIteratorByState(reads.iterator(), LocusIteratorByState.NO_DOWNSAMPLING,
                true, genomeLocParser, SampleListUtils.asSet(samples), false);


        final List<ReadBackedPileup> pileups = new LinkedList<>();
        final int startPos = activeRegionSpan.getStart();
        AlignmentContext next = libs.advanceToLocus(startPos, true);
        for ( int curPos = startPos; curPos <= activeRegionSpan.getStop(); curPos++ ) {
            if ( next != null && next.getLocation().getStart() == curPos ) {
                pileups.add(next.getBasePileup());
                next = libs.hasNext() ? libs.next() : null;
            } else {
                // no data, so we create empty pileups
                pileups.add(new ReadBackedPileupImpl(genomeLocParser.createGenomeLoc(activeRegionSpan.getContig(), curPos)));
            }
        }


    public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, GATKSAMIterator iterator, List<GenomeLoc> intervals, Collection<String> sampleNames) {
        this.sourceInfo = shard.getReadProperties();
        this.readIterator = new GATKSAMRecordIterator(iterator);


        this.libs = new LocusIteratorByState(readIterator,sourceInfo,genomeLocParser,sampleNames);
        this.sourceIterator = new PeekableIterator<AlignmentContext>(libs);


        this.intervalIterator = intervals.size()>0 ? new PeekableIterator<GenomeLoc>(intervals.iterator()) : null;
    }

Examples of org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState

Related Classes of org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState