List of advanceToLocus() Examples

Examples of advanceToLocus()

org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState.advanceToLocus()

Move this LIBS until we are over position Will return null if cannot reach position (because we run out of data in the locus) @param position the start position of the AlignmentContext we want back @param stopAtFirstNonEmptySiteAfterPosition if true, we will stop as soon as we find a context with data withposition >= position, otherwise we will return a null value and consume the data for the next position. This means that without specifying this value the LIBS will be in an indeterminate state after calling this function, and should be reconstructed from scratch for subsequent use @return a AlignmentContext at position, or null if this isn't possible

        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 {

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Examples of advanceToLocus()

Examples of org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState.advanceToLocus()