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.

    }


    private void stopWaitingToMerge() {
        if (vcfrWaitingToMerge == null) {
            if (!filteredVcfrList.isEmpty())
                throw new ReviewedGATKException("filteredVcfrList should be empty if not waiting to merge a vc!");
            return;
        }


        if (!emitOnlyMergedRecords || vcfrWaitingToMerge.resultedFromMerge)
            innerWriter.add(vcfrWaitingToMerge.vc);

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                            // Check MNPs vs. CHets:
                            if (containsRefAllele(site1Alleles) && containsRefAllele(site2Alleles)) {
                                logger.debug("HET-HET for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
                                if (logger.isDebugEnabled() && !(gt1.isHet() && gt2.isHet()))
                                    throw new ReviewedGATKException("Since !gt1.isHomRef() && !gt2.isHomRef(), yet both have ref alleles, they BOTH must be hets!");


                                // There's the potential to only have REF-ALT, ALT-REF (CHet), or possibly ALT-ALT together (MNP)
                                boolean hasMNP = false;


                                all2It = site2Alleles.iterator();

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        if ( ts < 0.0 || ts > 100.0)
            throw new UserException("Target FDR is unreasonable " + ts);


        if ( numKnown < 0 || numNovel < 0)
            throw new ReviewedGATKException("Invalid tranche - no. variants is < 0 : known " + numKnown + " novel " + numNovel);


        if ( name == null )
            throw new ReviewedGATKException("BUG -- name cannot be null");
    }

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        return hasNext;
    }


    public int[] next() {
        if (!hasNext())
            throw new ReviewedGATKException("CANNOT iterate past end!");


        // Copy the assignment to be returned:
        int[] nextList = new int[valList.length];
        for (int i = 0; i < valList.length; i++)
            nextList[i] = valList[i];

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    public GenomeLoc getGenomeLoc() {
        return loc;
    }
    public int compareTo(final Object o) {
        if (!(o instanceof GenomeEvent))
            throw new ReviewedGATKException("BUG: comparing variant context with non-VC object");


        GenomeEvent otherEvent = (GenomeEvent)o;


         return loc.compareTo(otherEvent.getGenomeLoc());
    }

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                final double chi2PValue = new ChiSquareTestImpl().chiSquareTest(counts);
                final double penalty = -10.0 * Math.log10(Math.max(chi2PValue, SMALLEST_CHI2_PVALUE));


                // make sure things are reasonable and fail early if not
                if (Double.isInfinite(penalty) || Double.isNaN(penalty))
                    throw new ReviewedGATKException("chi2 value is " + chi2PValue + " at " + getRecalDatum());


                return penalty;
            } catch ( MathException e ) {
                throw new ReviewedGATKException("Failed in calculating chi2 value", e);
            }
        }
    }

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        this.nObservationsPerQual = nObservationsPerQual;
        this.nLevels = nLevels;
        this.minInterestingQual = minInterestingQual;


        // some sanity checking
        if ( Collections.min(nObservationsPerQual) < 0 ) throw new ReviewedGATKException("Quality score histogram has negative values at: " + Utils.join(", ", nObservationsPerQual));
        if ( nLevels < 0 ) throw new ReviewedGATKException("nLevels must be >= 0");
        if ( minInterestingQual < 0 ) throw new ReviewedGATKException("minInterestingQual must be >= 0");


        // actually run the quantizer
        this.quantizedIntervals = quantize();


        // store the map

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                map.set(q, interval.getQual());
            }
        }


        if ( Collections.min(map) == Byte.MIN_VALUE )
            throw new ReviewedGATKException("quantized quality score map contains an un-initialized value");


        return map;
    }

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        public QualInterval merge(final QualInterval toMerge) {
            final QualInterval left = this.compareTo(toMerge) < 0 ? this : toMerge;
            final QualInterval right = this.compareTo(toMerge) < 0 ? toMerge : this;


            if ( left.qEnd + 1 != right.qStart )
                throw new ReviewedGATKException("Attempting to merge non-contiguous intervals: left = " + left + " right = " + right);


            final long nCombinedObs = left.nObservations + right.nObservations;
            final long nCombinedErr = left.nErrors + right.nErrors;


            final int level = Math.max(left.level, right.level) + 1;

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     * Create a new object
     * @param logger        logger
     * @param UAC           unified arg collection
     */
    protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
        if ( logger == null || UAC == null ) throw new ReviewedGATKException("Bad arguments");
        this.UAC = UAC;
        this.logger = logger;
    }

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