Examples with IntervalListScatterer org.broadinstitute.hellbender.tools.picard.interval.IntervalListScatterer used on opensource projects

Example 1 with IntervalListScatterer

use of org.broadinstitute.hellbender.tools.picard.interval.IntervalListScatterer in project gatk by broadinstitute.

the class SplitIntervals method onTraversalStart.

@Override
public void onTraversalStart() {
    ParamUtils.isPositive(scatterCount, "scatter count must be > 0.");
    if (!outputDir.exists() && !outputDir.mkdir()) {
        throw new RuntimeIOException("Unable to create directory: " + outputDir.getAbsolutePath());
    }
    // in general dictionary will be from the reference, but using -I reads.bam or -F variants.vcf
    // to use the sequence dict from a bam or vcf is also supported
    final SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
    final List<SimpleInterval> intervals = hasIntervals() ? intervalArgumentCollection.getIntervals(sequenceDictionary) : IntervalUtils.getAllIntervalsForReference(sequenceDictionary);
    final IntervalList intervalList = new IntervalList(sequenceDictionary);
    intervals.stream().map(si -> new Interval(si.getContig(), si.getStart(), si.getEnd())).forEach(intervalList::add);
    final IntervalListScatterer scatterer = new IntervalListScatterer(subdivisionMode);
    final List<IntervalList> scattered = scatterer.scatter(intervalList, scatterCount, false);
    final DecimalFormat formatter = new DecimalFormat("0000");
    IntStream.range(0, scattered.size()).forEach(n -> scattered.get(n).write(new File(outputDir, formatter.format(n) + "-scattered.intervals")));
}

Example 2 with IntervalListScatterer

use of org.broadinstitute.hellbender.tools.picard.interval.IntervalListScatterer in project gatk-protected by broadinstitute.

the class SplitIntervals method onTraversalStart.

@Override
public void onTraversalStart() {
    ParamUtils.isPositive(scatterCount, "scatter count must be > 0.");
    if (!outputDir.exists() && !outputDir.mkdir()) {
        throw new RuntimeIOException("Unable to create directory: " + outputDir.getAbsolutePath());
    }
    // in general dictionary will be from the reference, but using -I reads.bam or -F variants.vcf
    // to use the sequence dict from a bam or vcf is also supported
    final SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
    final List<SimpleInterval> intervals = hasIntervals() ? intervalArgumentCollection.getIntervals(sequenceDictionary) : IntervalUtils.getAllIntervalsForReference(sequenceDictionary);
    final IntervalList intervalList = new IntervalList(sequenceDictionary);
    intervals.stream().map(si -> new Interval(si.getContig(), si.getStart(), si.getEnd())).forEach(intervalList::add);
    final IntervalListScatterer scatterer = new IntervalListScatterer(subdivisionMode);
    final List<IntervalList> scattered = scatterer.scatter(intervalList, scatterCount, false);
    final DecimalFormat formatter = new DecimalFormat("0000");
    IntStream.range(0, scattered.size()).forEach(n -> scattered.get(n).write(new File(outputDir, formatter.format(n) + "-scattered.intervals")));
}