Package org.broadinstitute.gatk.utils.exceptions

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


    private void checkArgumentsValues() {
        checkInputReportFile("BQSR",bqsrFile);
        checkInputReportFile("before",beforeFile);
        checkInputReportFile("after",afterFile);
        if (bqsrFile == null && beforeFile == null && afterFile == null) {
            throw new UserException("you must provide at least one recalibration report file "
                    + "(arguments -BQSR, -" + BEFORE_ARG_SHORT_NAME + " or -" + AFTER_ARG_SHORT_NAME);
        }

        checkOutputFile(PDF_ARG_SHORT_NAME,pdfFile);
        checkOutputFile(CSV_ARG_SHORT_NAME, csvFile);
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     *
     * @throw UserException if no output was requested.
     */
    private void checkOutputRequested() {
        if (pdfFile == null && csvFile == null) {
            throw new UserException("you need to request at least one output:"
                    + " the intermediate csv file (-" + CSV_ARG_SHORT_NAME + " FILE)"
                    + " or the final plot file (-" + PDF_ARG_SHORT_NAME + " FILE).");
        }
    }
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    private void generateCsvFile(final File csvFile, final Map<String, RecalibrationReport> reports) {
        try {
            logger.info("Generating csv file '" + csvFile + "'");
            RecalUtils.generateCsv(csvFile, reports);
        } catch (FileNotFoundException e) {
            throw new UserException(
                    String.format("There is a problem creating the intermediary Csv file '%s': %s",
                            csvFile,e.getMessage()),e);
        }
    }
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            try {
              final File result = File.createTempFile("AnalyzeCovariates", ".csv");
              result.deleteOnExit();
              return result;
            } catch (IOException e) {
                throw new UserException("Could not create temporary Csv file",e);
            }
        }
    }
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            throw new UserException.BadArgumentValue("indels_context_size", String.format("context size cannot be bigger than %d, but was %d", MAX_DNA_CONTEXT, indelsContextSize));

        LOW_QUAL_TAIL = RAC.LOW_QUAL_TAIL;
       
        if (mismatchesContextSize <= 0 || indelsContextSize <= 0)
            throw new UserException(String.format("Context size must be positive, if you don't want to use the context covariate, just turn it off instead. Mismatches: %d Indels: %d", mismatchesContextSize, indelsContextSize));

        mismatchesKeyMask = createMask(mismatchesContextSize);
        indelsKeyMask = createMask(indelsContextSize);
    }
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        if ( remappedAlleles == null || remappedAlleles.size() == 0 ) throw new IllegalArgumentException("The list of input alleles must not be null or empty");
        if ( targetAlleles == null || targetAlleles.size() == 0 ) throw new IllegalArgumentException("The list of target alleles must not be null or empty");

        if ( !remappedAlleles.contains(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) )
            throw new UserException("The list of input alleles must contain " + GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE + " as an allele but that is not the case at position " + position + "; please use the Haplotype Caller with gVCF output to generate appropriate records");
        final int indexOfGenericAlt = remappedAlleles.indexOf(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);

        final int[] indexMapping = new int[targetAlleles.size()];

        // the reference alleles always match up (even if they don't appear to)
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    private void precomputeInverse() {
        try {
            cachedSigmaInverse = sigma.inverse();
        } catch( Exception e ) {
            throw new UserException("Error during clustering. Most likely there are too few variants used during Gaussian mixture modeling. Please consider raising the number of variants used to train the negative model (via --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example).");
        }
    }
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            doNotRunPhysicalPhasing = true;
            logger.info("Currently, physical phasing is not available when ploidy is different than " + HomoSapiensConstants.DEFAULT_PLOIDY + "; therefore it won't be performed");
        }

        if (dontGenotype && emitReferenceConfidence())
            throw new UserException("You cannot request gVCF output and do not genotype at the same time");

        if ( emitReferenceConfidence() ) {

            if (SCAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES)
                throw new UserException.BadArgumentValue("ERC/gt_mode","you cannot request reference confidence output and GENOTYPE_GIVEN_ALLELES at the same time");

            SCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = -0.0;
            SCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = -0.0;

            // also, we don't need to output several of the annotations
            annotationsToExclude.add("ChromosomeCounts");
            annotationsToExclude.add("FisherStrand");
            annotationsToExclude.add("StrandOddsRatio");
            annotationsToExclude.add("QualByDepth");

            // but we definitely want certain other ones
            annotationsToUse.add("StrandBiasBySample");
            logger.info("Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output");
            if (!SCAC.annotateAllSitesWithPLs)
                logger.info("All sites annotated with PLs forced to true for reference-model confidence output");
            SCAC.annotateAllSitesWithPLs = true;
        } else if ( ! doNotRunPhysicalPhasing ) {
            doNotRunPhysicalPhasing = true;
            logger.info("Disabling physical phasing, which is supported only for reference-model confidence output");
        }

        final GenomeAnalysisEngine toolkit = getToolkit();
        samplesList = toolkit.getReadSampleList();
        Set<String> sampleSet = SampleListUtils.asSet(samplesList);

        if (sampleNameToUse != null) {
            if (!sampleSet.contains(sampleNameToUse))
                throw new UserException.BadArgumentValue("sample_name", "Specified name does not exist in input bam files");
            if (sampleSet.size() == 1) {
                //No reason to incur performance penalty associated with filtering if they specified the name of the only sample
                sampleNameToUse = null;
            } else {
                samplesList = new IndexedSampleList(sampleNameToUse);
                sampleSet = SampleListUtils.asSet(samplesList);
            }
        }


        // create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
        final UnifiedArgumentCollection simpleUAC = SCAC.cloneTo(UnifiedArgumentCollection.class);
        simpleUAC.outputMode = OutputMode.EMIT_VARIANTS_ONLY;
        simpleUAC.genotypingOutputMode = GenotypingOutputMode.DISCOVERY;
        simpleUAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = Math.min( 4.0, SCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING ); // low values used for isActive determination only, default/user-specified values used for actual calling
        simpleUAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, SCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling
        simpleUAC.CONTAMINATION_FRACTION = 0.0;
        simpleUAC.CONTAMINATION_FRACTION_FILE = null;
        simpleUAC.exactCallsLog = null;
        // Seems that at least with some test data we can lose genuine haploid variation if we use
        // UGs engine with ploidy == 1
        simpleUAC.genotypeArgs.samplePloidy = Math.max(2,SCAC.genotypeArgs.samplePloidy);

        activeRegionEvaluationGenotyperEngine = new UnifiedGenotypingEngine(simpleUAC,
                FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),simpleUAC,logger), toolkit);
        activeRegionEvaluationGenotyperEngine.setLogger(logger);

        if( SCAC.CONTAMINATION_FRACTION_FILE != null )
            SCAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(SCAC.CONTAMINATION_FRACTION_FILE, SCAC.CONTAMINATION_FRACTION, sampleSet, logger));

        if( SCAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES && consensusMode )
            throw new UserException("HaplotypeCaller cannot be run in both GENOTYPE_GIVEN_ALLELES mode and in consensus mode at the same time. Please choose one or the other.");

        final GenomeLocParser genomeLocParser = toolkit.getGenomeLocParser();

        genotypingEngine = new HaplotypeCallerGenotypingEngine( SCAC, samplesList, genomeLocParser, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),SCAC,logger), !doNotRunPhysicalPhasing);
        // initialize the output VCF header
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                return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate, heterogeneousKmerSizeResolution,SCAC.DEBUG,debugGraphTransformations);
            case Random:
                return new RandomLikelihoodCalculationEngine();
            default:
                //Note: we do not include in the error message list as it is of no grand public interest.
                throw new UserException("Unsupported likelihood calculation engine '" + likelihoodCalculationEngine +
                        "'. Please use one of the following instead: 'PairHMM' or 'GraphBased'.");
        }
    }
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            trios = ((Walker) walker).getSampleDB().getTrios();
            if ( trios.size() > 0 ) {
                mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
            }
            else {
                throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator, and must be provided a valid PED file (-ped) from the command line.");
            }
        }

        Map<String,Object> attributeMap = new HashMap<String,Object>(1);
        //double pNoMV = 1.0;
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