Examples with GVCFWriter org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter used on opensource projects

Example 1 with GVCFWriter

use of org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter in project gatk by broadinstitute.

the class HaplotypeCallerEngine method makeVCFWriter.

/**
     * Create a VCF or GVCF writer as appropriate, given our arguments
     *
     * @param outputVCF location to which the vcf should be written
     * @param readsDictionary sequence dictionary for the reads
     * @return a VCF or GVCF writer as appropriate, ready to use
     */
public VariantContextWriter makeVCFWriter(final String outputVCF, final SAMSequenceDictionary readsDictionary) {
    Utils.nonNull(outputVCF);
    Utils.nonNull(readsDictionary);
    VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(new File(outputVCF), readsDictionary, false);
    if (hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.GVCF) {
        try {
            writer = new GVCFWriter(writer, hcArgs.GVCFGQBands, hcArgs.genotypeArgs.samplePloidy);
        } catch (IllegalArgumentException e) {
            throw new CommandLineException.BadArgumentValue("GQBands", "are malformed: " + e.getMessage());
        }
    }
    return writer;
}

Example 2 with GVCFWriter

use of org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter in project gatk-protected by broadinstitute.

the class HaplotypeCallerEngine method makeVCFWriter.

/**
     * Create a VCF or GVCF writer as appropriate, given our arguments
     *
     * @param outputVCF location to which the vcf should be written
     * @param readsDictionary sequence dictionary for the reads
     * @return a VCF or GVCF writer as appropriate, ready to use
     */
public VariantContextWriter makeVCFWriter(final String outputVCF, final SAMSequenceDictionary readsDictionary) {
    Utils.nonNull(outputVCF);
    Utils.nonNull(readsDictionary);
    VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(new File(outputVCF), readsDictionary, false);
    if (hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.GVCF) {
        try {
            writer = new GVCFWriter(writer, hcArgs.GVCFGQBands, hcArgs.genotypeArgs.samplePloidy);
        } catch (IllegalArgumentException e) {
            throw new CommandLineException.BadArgumentValue("GQBands", "are malformed: " + e.getMessage());
        }
    }
    return writer;
}