Examples of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

Package org.broadinstitute.gatk.utils.exceptions

Examples of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
A trivial extension around GATKException to mark exceptions that have been reviewed for correctness, completeness, etc. By using this exception you are saying "this is the right error message". GATKException is now just a catch all for lazy users.


                        if (phasedCurGenotypeRelativeToPrevious) {
                            Genotype prevHetGenotype = phaseWindow.phaseRelativeToGenotype();
                            SNPallelePair prevAllelePair = new SNPallelePair(prevHetGenotype);
                            if (!prevHetGenotype.hasAnyAttribute(HP_KEY))
                                throw new ReviewedGATKException("Internal error: missing haplotype markings for previous genotype, even though we put it there...");
                            String[] prevPairNames = (String[]) prevHetGenotype.getAnyAttribute(HP_KEY);


                            String[] curPairNames = ensurePhasing(allelePair, prevAllelePair, prevPairNames, pr.haplotype);
                            Genotype phasedGt = new GenotypeBuilder(gt)
                                    .alleles(allelePair.getAllelesAsList())

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        Ensure that curAllelePair is phased relative to prevAllelePair as specified by hap.
     */


    public static String[] ensurePhasing(SNPallelePair curAllelePair, SNPallelePair prevAllelePair, String[] prevPairNames, Haplotype hap) {
        if (hap.size() < 2)
            throw new ReviewedGATKException("LOGICAL ERROR: Only considering haplotypes of length > 2!");


        String[] curPairNames = prevPairNames;


        byte prevBase = hap.getBase(0); // The 1st base in the haplotype
        byte curBase = hap.getBase(1);  // The 2nd base in the haplotype

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        // ASSUMES that: isUnfilteredCalledDiploidGenotype(vrGt) && vrGt.isHet() [vrGt = vr.variant.getGenotype(sample)]


        public PhasingWindow(VariantAndReads vr, String sample, List<GenotypeAndReadBases> prevHetGenotypes, int goBackFromEndOfPrevHets) {
            if (prevHetGenotypes.isEmpty() || goBackFromEndOfPrevHets >= prevHetGenotypes.size()) // no previous sites against which to phase
                throw new ReviewedGATKException("Should never get empty set of previous sites to phase against");


            // Include these previously phased sites in the phasing computation:
            List<GenotypeAndReadBases> listHetGenotypes = new LinkedList<GenotypeAndReadBases>(prevHetGenotypes);


            phaseRelativeToIndex = listHetGenotypes.size() - 1 - goBackFromEndOfPrevHets;

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            case INDEL:
                return evalVC.isStructuralIndel() || evalVC.isIndel() || evalVC.isMixed() || evalVC.isSymbolic();
            case BOTH:
                return true;
            default:
                throw new ReviewedGATKException( "Encountered unknown recal mode: " + mode );
        }
    }

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           where the other allele is chosen at each site
         */
        private Haplotype complement(Haplotype hap) {
            int numSites = SNPallelePairs.length;
            if (hap.size() != numSites)
                throw new ReviewedGATKException("INTERNAL ERROR: hap.size() != numSites");


            // Take the other base at EACH position of the Haplotype:
            byte[] complementBases = new byte[numSites];
            for (int i = 0; i < numSites; i++)
                complementBases[i] = SNPallelePairs[i].getOtherBase(hap.getBase(i));

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    private Allele top;
    private Allele bottom;


    public AllelePair(Genotype gt) {
        if (gt.getPloidy() != 2)
            throw new ReviewedGATKException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString());


        this.top = gt.getAllele(0);
        this.bottom = gt.getAllele(1);
    }

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        if (logLikelihoods == null){
            log10Likelihoods = new double[likelihoodDim]; 
            Arrays.fill(log10Likelihoods, MIN_LIKELIHOOD);
        } else {
            if (logLikelihoods.length != likelihoodDim)
                throw new ReviewedGATKException("BUG: inconsistent parameters when creating GeneralPloidyGenotypeLikelihoods object");


            log10Likelihoods = logLikelihoods; //.clone(); // is clone needed?
        }
        fillCache();
        LOG10_PLOIDY = Math.log10((double)numChromosomes);

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        public void setInitialStateVector(final int[] stateVector) {
            if (restrictSumTo > 0) {
                // check that desired vector is valid
                if (MathUtils.sum(stateVector) != restrictSumTo)
                    throw new ReviewedGATKException("BUG: initial state vector nor compatible with sum iterator");


                final int numAlleles = currentState.length;
                final int ploidy = restrictSumTo;


                linearIndex = GeneralPloidyGenotypeLikelihoods.getLinearIndex(stateVector, numAlleles, ploidy);
            }
            else
                throw new ReviewedGATKException("BUG: Not supported");


        }

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                if (a.isReference())
                    refAllele = a;
            }


            if (refAllele == null)
                throw new ReviewedGATKException("BUG: no ref alleles in passed in allele list!");


            // count number of elements in pileup
            for (PileupElement elt : pileup) {
                if (VERBOSE)
                    System.out.format("base:%s isNextToDel:%b isNextToIns:%b eventBases:%s eventLength:%d\n",elt.getBase(), elt.isBeforeDeletionStart(),elt.isBeforeInsertion(),elt.getBasesOfImmediatelyFollowingInsertion(),elt.getLengthOfImmediatelyFollowingIndel());

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     * @param locus      The locus given as a GenomeLoc
     * @param pileup     The pileup of that locus, this exclusively contains the sample
     */
    public void addLocus(GenomeLoc locus, ReadBackedPileup pileup) {
        if (!interval.containsP(locus))
            throw new ReviewedGATKException(String.format("Locus %s is not part of the Interval %s", locus, interval));


        // a null pileup means there nothing to add
        if (pileup != null) {
            final int locusIndex = locus.getStart() - interval.getStart();
            final int rawCoverage = pileup.depthOfCoverage();

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