Examples of SAMPileupFeature

    @Argument(fullName="continue_after_error",doc="Continue after encountering an error",required=false)
    public boolean CONTINUE_AFTER_AN_ERROR = false;


    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        ReadBackedPileup pileup = context.getBasePileup();
        SAMPileupFeature truePileup = getTruePileup( tracker );


        if ( truePileup == null ) {
            out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBaseAsChar()));
            if ( ! CONTINUE_AFTER_AN_ERROR ) {
                throw new UserException.BadInput(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
                        context.getLocation(), new String(pileup.getBases())));
            }
        } else {
            String pileupDiff = pileupDiff(pileup, truePileup, true);
            if ( pileupDiff != null ) {
                out.printf("%s vs. %s%n", pileup.getPileupString(ref.getBaseAsChar()), truePileup.getPileupString());
                if ( ! CONTINUE_AFTER_AN_ERROR ) {
                    throw new UserException.BadInput(String.format("The input pileup doesn't match the GATK's internal pileup: %s", pileupDiff));
                }
            }
        }

     * assumes that the genotype will only be point or indel.
     * @param tracker ROD tracker from which to extract pileup data.
     * @return True pileup data.
     */
    private SAMPileupFeature getTruePileup( RefMetaDataTracker tracker ) {
        SAMPileupFeature pileupArg = tracker.getFirstValue(pileup);


        if( pileupArg == null)
            return null;


        if( pileupArg.hasPointGenotype() )
            return pileupArg.getPointGenotype();
        else if( pileupArg.hasIndelGenotype() )
            return pileupArg.getIndelGenotype();
        else
            throw new ReviewedGATKException("Unsupported pileup type: " + pileupArg);
    }

Examples of SAMPileupFeature

Examples of org.broadinstitute.gatk.utils.codecs.sampileup.SAMPileupFeature

Examples of org.broadinstitute.gatk.utils.codecs.sampileup.SAMPileupFeature