Examples with VariantContextBuilder htsjdk.variant.variantcontext.VariantContextBuilder used on opensource projects

Example 6 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder in project gatk-protected by broadinstitute.

the class ReferenceBasesUnitTest method test.

@Test
public void test() {
    final File refFasta = new File(b37_reference_20_21);
    final ReferenceDataSource refDataSource = new ReferenceFileSource(refFasta);
    final ReferenceContext ref = new ReferenceContext(refDataSource, new SimpleInterval("20", 10_000_000, 10_000_200));
    final VariantContext vc = new VariantContextBuilder("source", "20", 10_000_100, 10_000_100, Collections.singleton(Allele.create((byte) 'A', true))).make();
    final String refBases = (String) new ReferenceBases().annotate(ref, vc, null).get(ReferenceBases.REFERENCE_BASES_KEY);
    Assert.assertEquals(refBases, "ACTGCATCCCTTGCATTTCC");
}

Example 7 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder in project gatk by broadinstitute.

the class RMSMappingQuality method finalizeRawMQ.

/**
     * converts {@link GATKVCFConstants#RAW_RMS_MAPPING_QUALITY_KEY} into  {@link VCFConstants#RMS_MAPPING_QUALITY_KEY}  annotation if present
     * @param vc which potentially contains rawMQ
     * @return if vc contained {@link GATKVCFConstants#RAW_RMS_MAPPING_QUALITY_KEY} it will be replaced with {@link VCFConstants#RMS_MAPPING_QUALITY_KEY}
     * otherwise return the original vc
     */
public VariantContext finalizeRawMQ(final VariantContext vc) {
    final String rawMQdata = vc.getAttributeAsString(getRawKeyName(), null);
    if (rawMQdata == null) {
        return vc;
    } else {
        final double squareSum = parseRawDataString(rawMQdata);
        final int numOfReads = getNumOfReads(vc);
        final double rms = Math.sqrt(squareSum / (double) numOfReads);
        final String finalizedRMSMAppingQuality = formattedValue(rms);
        return new VariantContextBuilder(vc).rmAttribute(getRawKeyName()).attribute(getKeyNames().get(0), finalizedRMSMAppingQuality).make();
    }
}

Example 8 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder in project gatk by broadinstitute.

the class GenotypeConcordanceTest method testGenotypeConcordanceDetermineState.

@Test(dataProvider = "genotypeConcordanceDetermineStateDataProvider")
public void testGenotypeConcordanceDetermineState(final Allele truthAllele1, final Allele truthAllele2, final TruthState expectedTruthState, final Allele callAllele1, final Allele callAllele2, final CallState expectedCallState) throws Exception {
    final List<Allele> truthAlleles = makeUniqueListOfAlleles(truthAllele1, truthAllele2);
    final Genotype truthGt = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(truthAllele1, truthAllele2));
    final VariantContext truthVariantContext = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, truthAlleles).genotypes(truthGt).make();
    final List<Allele> callAlleles = makeUniqueListOfAlleles(callAllele1, callAllele2);
    final Genotype callGt = GenotypeBuilder.create(CALL_SAMPLE_NAME, Arrays.asList(callAllele1, callAllele2));
    final VariantContext callVariantContext = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, callAlleles).genotypes(callGt).make();
    testGenotypeConcordanceDetermineState(truthVariantContext, expectedTruthState, callVariantContext, expectedCallState, 0, 0);
}

Example 9 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder in project gatk by broadinstitute.

the class GenotypeConcordanceTest method testGenotypeConcordanceDetermineStateFilter.

@Test
public void testGenotypeConcordanceDetermineStateFilter() throws Exception {
    final Set<String> filters = new HashSet<>(Arrays.asList("BAD!"));
    // Filtering on the variant context
    final List<Allele> alleles1 = makeUniqueListOfAlleles(Aref, C);
    final Genotype gt1 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
    final VariantContext vcFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles1).genotypes(gt1).filters(filters).make();
    final List<Allele> alleles2 = makeUniqueListOfAlleles(Aref, T);
    final Genotype gt2 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, T));
    final VariantContext vcNotFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles2).genotypes(gt2).make();
    testGenotypeConcordanceDetermineState(vcFiltered, TruthState.VC_FILTERED, vcNotFiltered, CallState.HET_REF_VAR1, 0, 0);
    testGenotypeConcordanceDetermineState(vcNotFiltered, TruthState.HET_REF_VAR1, vcFiltered, CallState.VC_FILTERED, 0, 0);
    testGenotypeConcordanceDetermineState(vcFiltered, TruthState.VC_FILTERED, vcFiltered, CallState.VC_FILTERED, 0, 0);
    // Filtering on the genotype
    final List<String> gtFilters = new ArrayList<>(Arrays.asList("WICKED"));
    final List<Allele> alleles3 = makeUniqueListOfAlleles(Aref, C);
    final Genotype gt3 = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).filters(gtFilters).make();
    final VariantContext vcGtFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles3).genotypes(gt3).make();
    testGenotypeConcordanceDetermineState(vcGtFiltered, TruthState.GT_FILTERED, vcNotFiltered, CallState.HET_REF_VAR1, 0, 0);
    testGenotypeConcordanceDetermineState(vcNotFiltered, TruthState.HET_REF_VAR1, vcGtFiltered, CallState.GT_FILTERED, 0, 0);
    testGenotypeConcordanceDetermineState(vcGtFiltered, TruthState.GT_FILTERED, vcGtFiltered, CallState.GT_FILTERED, 0, 0);
}

Example 10 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder in project gatk by broadinstitute.

the class GenotypeConcordanceTest method testGenotypeConcordanceDetermineStateGq.

@Test
public void testGenotypeConcordanceDetermineStateGq() throws Exception {
    final List<Allele> allelesNormal = makeUniqueListOfAlleles(Aref, C);
    final Genotype gtNormal = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
    final VariantContext vcNormal = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesNormal).genotypes(gtNormal).make();
    final List<Allele> allelesLowGq = makeUniqueListOfAlleles(Aref, C);
    final Genotype gtLowGq = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).GQ(4).make();
    final VariantContext vcLowGq = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesLowGq).genotypes(gtLowGq).make();
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.LOW_GQ, vcNormal, CallState.HET_REF_VAR1, 20, 0);
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
    testGenotypeConcordanceDetermineState(vcNormal, TruthState.HET_REF_VAR1, vcLowGq, CallState.LOW_GQ, 20, 0);
    testGenotypeConcordanceDetermineState(vcNormal, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.LOW_GQ, vcLowGq, CallState.LOW_GQ, 20, 0);
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
}