Package org.broadinstitute.gatk.utils.exceptions

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

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     * Controls whether to index this output stream on-the-fly.
     * @param indexOnTheFly True means create an index.  False means skip index creation.
     */
    public void setIndexOnTheFly( boolean indexOnTheFly ) {
        if(writeStarted)
            throw new UserException("Attempted to index a BAM on the fly of a file with alignments already in it.");
        this.indexOnTheFly = indexOnTheFly;
    }
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     * Gets whether to generate an md5 on-the-fly for this BAM.
     * @param generateMD5   True generates the md5.  False means skip writing the file.
     */
    public void setGenerateMD5(boolean generateMD5) {
        if(writeStarted)
            throw new UserException("Attempted to turn on md5 generation for BAM file with alignments already in it.");       
        this.generateMD5 = generateMD5;
    }
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                    val = Utils.join(",", toVal);
                }

                addFieldValue(val, records);
            } else if ( ! allowMissingData ) {
                throw new UserException(String.format("Missing field %s in vc %s at %s", field, vc.getSource(), vc));
            } else {
                addFieldValue(MISSING_DATA, records);
            }
        }
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            Genotype evalGenotype = eval.getGenotype(sample);
            Genotype truthGenotype = truth.getGenotype(sample);
            // ensure genotypes are either no-call ("."), missing (empty alleles), or diploid
            if ( ( ! evalGenotype.isNoCall() && evalGenotype.getPloidy() != 2 && evalGenotype.getPloidy() > 0) ||
                 ( ! truthGenotype.isNoCall() && truthGenotype.getPloidy() != 2 && truthGenotype.getPloidy() > 0) ) {
                throw new UserException(String.format("Concordance Metrics is currently only implemented for DIPLOID genotypes, found eval ploidy: %d, comp ploidy: %d",evalGenotype.getPloidy(),truthGenotype.getPloidy()));
            }
            perSampleGenotypeConcordance.get(sample).update(evalGenotype,truthGenotype,alleleTruth,truthRef);
            doPrint = overallGenotypeConcordance.update(evalGenotype,truthGenotype,alleleTruth,truthRef);
            if(sitesFile != null && doPrint)
                sitesFile.println(eval.getChr() + ":" + eval.getStart() + "\t" + sample + "\t" + truthGenotype.getType() + "\t" + evalGenotype.getType());
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        final Walker artWalker = new RunReportDummyActiveRegionWalker();

        final Exception noException = null;
        final Exception javaException = new IllegalArgumentException("javaException");
        final Exception stingException = new ReviewedGATKException("GATKException");
        final Exception userException = new UserException("userException");

        final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
        engine.setArguments(new GATKArgumentCollection());

        for ( final Walker walker : Arrays.asList(readWalker, lociWalker, rodWalker, artWalker) ) {
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            final Tags tags = parser.getTags(fileName);
            fileName = expandFileName(fileName);

            List<String> positionalTags = tags.getPositionalTags();
            if(positionalTags.size() != 2)
                throw new UserException("Invalid syntax for -B (reference-ordered data) input flag.  " +
                        "Please use the following syntax when providing reference-ordered " +
                        "data: -B:<name>,<type> <filename>.");
            // Assume that if tags are present, those tags are name and type.
            // Name is always first, followed by type.
            String name = positionalTags.get(0);
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                break;

            case SOFTCLIP_BASES:
                if (read.getReadUnmappedFlag()) {
                    // we can't process unmapped reads
                    throw new UserException("Read Clipper cannot soft clip unmapped reads");
                }

                //System.out.printf("%d %d %d%n", stop, start, read.getReadLength());
                int myStop = stop;
                if ((stop + 1 - start) == read.getReadLength()) {
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                } else {
                    start = parsePosition(str.substring(colonIndex + 1, dashIndex));  // chr1:1-1
                    stop = parsePosition(str.substring(dashIndex + 1));
                }
            } catch(Exception e) {
                throw new UserException("Failed to parse Genome Location string: " + str, e);
            }
        }

        // is the contig valid?
        if (!contigIsInDictionary(contig))
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Related Classes of org.broadinstitute.gatk.utils.exceptions.UserException$MalformedWalkerArgumentsException

  • org.broadinstitute.gatk.engine.CommandLineExecutable
  • org.broadinstitute.gatk.engine.CommandLineGATK
  • org.broadinstitute.gatk.engine.datasources.reads.BAMSchedule
  • org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMReaders
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.PrintBAMRegion
  • org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod
  • org.broadinstitute.gatk.engine.filters.ReadGroupBlackListFilter
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