Examples with SAMPileupFeature org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature used on opensource projects

Example 1 with SAMPileupFeature

use of org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature in project gatk by broadinstitute.

the class CheckPileup method apply.

@Override
public void apply(final AlignmentContext context, final ReferenceContext ref, final FeatureContext featureContext) {
    final ReadPileup pileup = context.getBasePileup();
    final SAMPileupFeature truePileup = getTruePileup(featureContext);
    if (!ignoreOverlaps) {
        pileup.fixOverlaps();
    }
    if (truePileup == null) {
        out.printf("No truth pileup data available at %s%n", pileup.getPileupString((char) ref.getBase()));
        if (!continueAfterAnError) {
            throw new UserException.BadInput(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools mpileup data over all bases", context.getLocation(), new String(pileup.getBases())));
        }
    } else {
        final String pileupDiff = pileupDiff(pileup, truePileup);
        if (pileupDiff != null) {
            out.printf("%s vs. %s%n", pileup.getPileupString((char) ref.getBase()), truePileup.getPileupString());
            if (!continueAfterAnError) {
                throw new UserException.BadInput(String.format("The input pileup doesn't match the GATK's internal pileup: %s", pileupDiff));
            }
        }
    }
    nLoci++;
    nBases += pileup.size();
}