Package org.broadinstitute.gatk.engine.arguments

Examples of org.broadinstitute.gatk.engine.arguments.ValidationExclusion

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    protected MalformedReadFilter buildMalformedReadFilter(final boolean filterRNO) {
        return buildMalformedReadFiter(filterRNO,new ValidationExclusion.TYPE[] {});
    }

    protected MalformedReadFilter buildMalformedReadFiter(boolean filterRNO, final ValidationExclusion.TYPE... excl) {
        final ValidationExclusion ve = new ValidationExclusion(Arrays.asList(excl));

        final MalformedReadFilter filter = new MalformedReadFilter();

        final SAMFileHeader h = getHeader();
        final SAMDataSource ds =  getDataSource();
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        }

    }

    protected ValidationExclusion composeValidationExclusion() {
        return new ValidationExclusion();
    }
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        final Integer numFileHandles = 1; // I believe that any value would do but need to confirm.
        final boolean useOriginalBaseQualities = true;
        final ValidationStringency strictness = ValidationStringency.LENIENT;
        final Integer readBufferSize = 1; // not relevant.
        final DownsamplingMethod downsamplingMethod = DownsamplingMethod.NONE;
        final ValidationExclusion exclusionList = composeValidationExclusion();
        final Collection<ReadFilter> supplementalFilters = Collections.EMPTY_SET;
        final boolean includeReadsWithDeletionAtLoci = true;

        final GenomeLocParser glp = new GenomeLocParser(header.getSequenceDictionary());
        final SAMDataSource res = new SAMDataSource(
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    private boolean allowNCigars;

    @Override
    public void initialize(final GenomeAnalysisEngine engine) {
        header = engine.getSAMFileHeader();
        ValidationExclusion validationExclusions = null;
        final SAMDataSource rds = engine.getReadsDataSource();
        if (rds != null) {
          final ReadProperties rps = rds.getReadsInfo();
          if (rps != null) {
            validationExclusions = rps.getValidationExclusionList();
          }
        }
        if (validationExclusions == null) {
            allowNCigars = false;
        } else {
            allowNCigars = validationExclusions.contains(ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS);
        }
    }
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                genomeLocParser,
                false,
                ValidationStringency.STRICT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                false);
    }
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     * @param drivingDataSource Data on which to shard.
     * @param intervals intervals
     * @return the sharding strategy
     */
    protected Iterable<Shard> getShardStrategy(SAMDataSource readsDataSource, ReferenceSequenceFile drivingDataSource, GenomeLocSortedSet intervals) {
        ValidationExclusion exclusions = (readsDataSource != null ? readsDataSource.getReadsInfo().getValidationExclusionList() : null);
        DownsamplingMethod downsamplingMethod = readsDataSource != null ? readsDataSource.getReadsInfo().getDownsamplingMethod() : null;
        ReferenceDataSource referenceDataSource = this.getReferenceDataSource();

        // If reads are present, assume that accessing the reads is always the dominant factor and shard based on that supposition.
        if(!readsDataSource.isEmpty()) {
            if(!readsDataSource.hasIndex() && !exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
                throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed.  The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.");
            if(!readsDataSource.hasIndex() && intervals != null && !argCollection.allowIntervalsWithUnindexedBAM)
                throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available.");

            if(walker instanceof LocusWalker) {
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                genomeLocParser,
                argCollection.useOriginalBaseQualities,
                argCollection.strictnessLevel,
                argCollection.readBufferSize,
                downsamplingMethod,
                new ValidationExclusion(Arrays.asList(argCollection.unsafe)),
                filters,
                readTransformers,
                includeReadsWithDeletionAtLoci(),
                argCollection.defaultBaseQualities,
                removeProgramRecords,
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        this.readers = samFiles;
        this.header = header;
        this.sortOrder = sortOrder;
        this.validationStringency = strictness;
        this.downsamplingMethod = downsamplingMethod == null ? DownsamplingMethod.NONE : downsamplingMethod;
        this.exclusionList = exclusionList == null ? new ValidationExclusion() : exclusionList;
        this.supplementalFilters = supplementalFilters;
        this.readTransformers = readTransformers;
        this.includeReadsWithDeletionAtLoci = includeReadsWithDeletionAtLoci;
        this.useOriginalBaseQualities = useOriginalBaseQualities;
        this.defaultBaseQualities = defaultBaseQualities;
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        SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
                false,
                ValidationStringency.STRICT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                new ArrayList<ReadTransformer>(),
                false, (byte)30, false, true, null, IntervalMergingRule.ALL);

        engine.setReadsDataSource(dataSource);
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                new SAMFileHeader(),
                SAMFileHeader.SortOrder.coordinate,
                false,
                ValidationStringency.STRICT,
                downsamplingMethod,
                new ValidationExclusion(),
                Collections.<ReadFilter>emptyList(),
                Collections.<ReadTransformer>emptyList(),
                true,
                (byte) -1,
                keepReads);
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Related Classes of org.broadinstitute.gatk.engine.arguments.ValidationExclusion

  • org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSourceUnitTest
  • org.broadinstitute.gatk.engine.filters.AllowNCigarMalformedReadFilterUnitTest
  • org.broadinstitute.gatk.engine.filters.MalformedReadFilter
  • org.broadinstitute.gatk.engine.filters.MalformedReadFilterUnitTest
  • org.broadinstitute.gatk.engine.filters.ReadFilterTest
  • org.broadinstitute.gatk.engine.filters.UnsafeMalformedReadFilterUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.ReadMetricsUnitTest
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