Examples with AllelicCountCollection org.broadinstitute.hellbender.tools.copynumber.allelic.alleliccount.AllelicCountCollection used on opensource projects

Example 6 with AllelicCountCollection

use of org.broadinstitute.hellbender.tools.copynumber.allelic.alleliccount.AllelicCountCollection in project gatk by broadinstitute.

the class CollectAllelicCounts method doWork.

@Override
protected Object doWork() {
    validateArguments();
    final File referenceFile = referenceArguments.getReferenceFile();
    final IntervalList siteIntervals = IntervalList.fromFile(inputSiteIntervalsFile);
    final AllelicCountCollector allelicCountCollector = new AllelicCountCollector(referenceFile, readValidationStringency);
    logger.info("Collecting allelic counts...");
    final AllelicCountCollection allelicCounts = allelicCountCollector.collect(inputBAMFile, siteIntervals, minimumMappingQuality, minimumBaseQuality);
    allelicCounts.write(outputAllelicCountsFile);
    logger.info("Allelic counts written to " + outputAllelicCountsFile.toString());
    return "SUCCESS";
}