Examples with MendelianViolation org.broadinstitute.hellbender.utils.samples.MendelianViolation used on opensource projects

Example 1 with MendelianViolation

use of org.broadinstitute.hellbender.utils.samples.MendelianViolation in project gatk by broadinstitute.

the class SelectVariants method onTraversalStart.

/**
     * Set up the VCF writer, the sample expressions and regexs, filters inputs, and the JEXL matcher
     *
     */
@Override
public void onTraversalStart() {
    final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
    // Initialize VCF header lines
    final Set<VCFHeaderLine> headerLines = createVCFHeaderLineList(vcfHeaders);
    for (int i = 0; i < selectExpressions.size(); i++) {
        // It's not necessary that the user supply select names for the JEXL expressions, since those
        // expressions will only be needed for omitting records.  Make up the select names here.
        selectNames.add(String.format("select-%d", i));
    }
    jexls = VariantContextUtils.initializeMatchExps(selectNames, selectExpressions);
    // Prepare the sample names and types to be used by the corresponding filters
    samples = createSampleNameInclusionList(vcfHeaders);
    selectedTypes = createSampleTypeInclusionList();
    // Look at the parameters to decide which analysis to perform
    discordanceOnly = discordanceTrack != null;
    if (discordanceOnly) {
        logger.info("Selecting only variants discordant with the track: " + discordanceTrack.getName());
    }
    concordanceOnly = concordanceTrack != null;
    if (concordanceOnly) {
        logger.info("Selecting only variants concordant with the track: " + concordanceTrack.getName());
    }
    if (mendelianViolations) {
        sampleDB = initializeSampleDB();
        mv = new MendelianViolation(mendelianViolationQualThreshold, false, true);
    }
    selectRandomFraction = fractionRandom > 0;
    if (selectRandomFraction) {
        logger.info("Selecting approximately " + 100.0 * fractionRandom + "% of the variants at random from the variant track");
    }
    //TODO: this should be refactored/consolidated as part of
    // https://github.com/broadinstitute/gatk/issues/121 and
    // https://github.com/broadinstitute/gatk/issues/1116
    Set<VCFHeaderLine> actualLines = null;
    SAMSequenceDictionary sequenceDictionary = null;
    if (hasReference()) {
        File refFile = referenceArguments.getReferenceFile();
        sequenceDictionary = this.getReferenceDictionary();
        actualLines = VcfUtils.updateHeaderContigLines(headerLines, refFile, sequenceDictionary, suppressReferencePath);
    } else {
        sequenceDictionary = getHeaderForVariants().getSequenceDictionary();
        if (null != sequenceDictionary) {
            actualLines = VcfUtils.updateHeaderContigLines(headerLines, null, sequenceDictionary, suppressReferencePath);
        } else {
            actualLines = headerLines;
        }
    }
    vcfWriter = createVCFWriter(outFile);
    vcfWriter.writeHeader(new VCFHeader(actualLines, samples));
}