Package org.broadinstitute.gatk.engine.arguments

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

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        final 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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        final 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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        final 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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        final SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
                false,
                ValidationStringency.STRICT,
                null,
                null,
                new ValidationExclusion(),
                filters,
                new ArrayList<ReadTransformer>(),
                false, (byte)30, false, true, null, IntervalMergingRule.ALL);

        engine.setReadsDataSource(dataSource);
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public class AllowNCigarMalformedReadFilterUnitTest extends MalformedReadFilterUnitTest {


    @Override
    protected ValidationExclusion composeValidationExclusion() {
        return new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS));
    }
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public class UnsafeMalformedReadFilterUnitTest extends AllowNCigarMalformedReadFilterUnitTest {


    @Override
    protected ValidationExclusion composeValidationExclusion() {
        return new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL));
    }
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                genomeLocParser,
                false,
                ValidationStringency.SILENT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                false);

        Iterable<Shard> strat = data.createShardIteratorOverMappedReads(new LocusShardBalancer());
        int count = 0;
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                genomeLocParser,
                false,
                ValidationStringency.SILENT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                false);

        List<SAMProgramRecord> defaultProgramRecords = data.getHeader().getProgramRecords();
        assertTrue(defaultProgramRecords.size() != 0, "testRemoveProgramRecords: No program records found when using default constructor");

        boolean removeProgramRecords = false;
        data = new SAMDataSource(readers,
                new ThreadAllocation(),
                null,
                genomeLocParser,
                false,
                ValidationStringency.SILENT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                Collections.<ReadTransformer>emptyList(),
                false,
                (byte) -1,
                removeProgramRecords,
                false,
                null, IntervalMergingRule.ALL);

        List<SAMProgramRecord> dontRemoveProgramRecords = data.getHeader().getProgramRecords();
        assertEquals(dontRemoveProgramRecords, defaultProgramRecords, "testRemoveProgramRecords: default program records differ from removeProgramRecords = false");

        removeProgramRecords = true;
        data = new SAMDataSource(readers,
                new ThreadAllocation(),
                null,
                genomeLocParser,
                false,
                ValidationStringency.SILENT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                Collections.<ReadTransformer>emptyList(),
                false,
                (byte) -1,
                removeProgramRecords,
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                genomeLocParser,
                false,
                ValidationStringency.SILENT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                false);
    }
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                genomeLocParser,
                false,
                ValidationStringency.SILENT,
                null,
                null,
                new ValidationExclusion(),
                new ArrayList<ReadFilter>(),
                Collections.<ReadTransformer>emptyList(),
                false,
                (byte) -1,
                true,
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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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