Package org.broadinstitute.gatk.utils.exceptions

Examples of org.broadinstitute.gatk.utils.exceptions.UserException$MalformedVCF

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            }
        }

        // Unknown platforms
        else {
            throw new UserException("The platform (" + read.getReadGroup().getPlatform()
                    + ") associated with read group " + read.getReadGroup()
                    + " is not a recognized platform. Allowable options are " + NGSPlatform.knownPlatformsString());
        }
    }
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                                        final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
        if ( trios == null ) {
            if ( walker instanceof VariantAnnotator ) {
                trios =  ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents();
            } else {
                throw new UserException("Transmission disequilibrium test annotation can only be used from the Variant Annotator and requires a valid ped file be passed in.");
            }
        }

        final Map<String, Object> toRet = new HashMap<String, Object>(1);
        final HashSet<Sample> triosToTest = new HashSet<Sample>();
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    private int keyFromCycle(final int cycle) {
        // no negative values because values must fit into the first few bits of the long
        int result = Math.abs(cycle);
        if ( result > MAXIMUM_CYCLE_VALUE )
            throw new UserException("The maximum allowed value for the cycle is " + MAXIMUM_CYCLE_VALUE + ", but a larger cycle (" + result + ") was detected.  Please use the --maximum_cycle_value argument to increase this value (at the expense of requiring more memory to run)");

        result = result << 1; // shift so we can add the "sign" bit
        if ( cycle < 0 )
            result++; // negative cycles get the lower-most bit set
        return result;
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        if (readSamples.isEmpty()) {
            String noPhaseString = "No common samples in VCF and BAM headers" + (samplesToPhase == null ? "" : " (limited to sampleToPhase parameters)") + ", so nothing could possibly be phased!";
            if (permitNoSampleOverlap)
                logger.warn(noPhaseString);
            else
                throw new UserException(noPhaseString);
        }
    }
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            trios = ((Walker) walker).getSampleDB().getTrios();
            if ( trios.size() > 0 ) {
                mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
            }
            else {
                throw new UserException("Possible de novos annotation can only be used from the Variant Annotator, and must be provided a valid PED file (-ped) from the command line.");
            }
        }

        final Map<String,Object> attributeMap = new HashMap<String,Object>(1);
        boolean isHighConfDeNovo = false;
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        final GaussianMixtureModel badModel = engine.generateModel( negativeTrainingData, Math.min(VRAC.MAX_GAUSSIANS_FOR_NEGATIVE_MODEL, VRAC.MAX_GAUSSIANS));
        dataManager.dropAggregateData(); // Don't need the aggregate data anymore so let's free up the memory
        engine.evaluateData( dataManager.getData(), badModel, true );

        if( badModel.failedToConverge || goodModel.failedToConverge ) {
            throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --minNumBadVariants 5000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") );
        }

        engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel );

        // Find the VQSLOD cutoff values which correspond to the various tranches of calls requested by the user
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                        counter++;
                    }
                }
                break;
            default:
                throw new UserException(String.format("%d does not indicate a valid trio FamilyMember -- use 0 for mother, 1 for father, 2 for child",recalcInd));
        }

        recalcPosteriors[0] = MathUtils.log10sumLog10(marginalOverChangedHR,0);
        recalcPosteriors[1] = MathUtils.log10sumLog10(marginalOverChangedHET,0);
        recalcPosteriors[2] = MathUtils.log10sumLog10(marginalOverChangedHV,0);
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                    phasedAlleles.add(refAllele);
                else if(allele.isNonReference())
                    phasedAlleles.add(altAllele);
                    //At this point there should not be any other alleles left
                else
                    throw new UserException(String.format("BUG: Unexpected allele: %s. Please report.",allele.toString()));

            }

            //Compute the new Log10Error if the genotype is different from the original genotype
            double log10Error;
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     */
    private static int[] getAlleleCounts(final String VCFkey, final VariantContext context) {
        final Object alleleCountsFromVCF = context.getAttribute(VCFkey);
        if ( alleleCountsFromVCF instanceof List ) {
            if ( ((List) alleleCountsFromVCF).size() != context.getAlternateAlleles().size() )
                throw new UserException(String.format("Variant does not contain the same number of MLE allele counts as alternate alleles for record at %s:%d", context.getChr(), context.getStart()));
        }
        else if ( alleleCountsFromVCF instanceof String || alleleCountsFromVCF instanceof Integer) {//here length is 1
            if (context.getAlternateAlleles().size() != 1)
                throw new UserException(String.format("Variant does not contain the same number of MLE allele counts as alternate alleles for record at %s:%d", context.getChr(), context.getStart()));
        }
        return extractInts(alleleCountsFromVCF);
    }
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                }
            }
        }
        // check sizes
        if (nAlleles > MAX_NUM_ALLELES_TO_CACHE)
            throw new UserException("No support for this number of alleles");

        if (nSamplesPerPool > MAX_NUM_SAMPLES_PER_POOL)
            throw new UserException("No support for such large number of samples per pool");

        likelihoodDim = GenotypeLikelihoods.numLikelihoods(nAlleles, numChromosomes);

        if (logLikelihoods == null){
            log10Likelihoods = new double[likelihoodDim];
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