Examples with VariantContextWriter htsjdk.variant.variantcontext.writer.VariantContextWriter used on opensource projects

Example 31 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk by broadinstitute.

the class GVCFWriterUnitTest method writeGVCFToDisk.

@Test(dataProvider = "toWriteToDisk")
public void writeGVCFToDisk(List<VariantContext> variants, List<MinimalData> expected) {
    final List<Integer> gqPartitions = Arrays.asList(1, 10, 30);
    final File outputFile = createTempFile("generated", ".g.vcf");
    try (VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(outputFile, null, false);
        GVCFWriter gvcfWriter = new GVCFWriter(writer, gqPartitions, HomoSapiensConstants.DEFAULT_PLOIDY)) {
        gvcfWriter.writeHeader(getMinimalVCFHeader());
        variants.forEach(gvcfWriter::add);
    }
    assertGVCFIsParseableAndVariantsMatch(outputFile, expected);
}