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

Example 81 with VariantContextWriter

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

the class GATKToolUnitTest method testCreateVCFWriterLenientTrue.

@Test(dataProvider = "createVCFWriterLenientData")
public void testCreateVCFWriterLenientTrue(final File inputFile, final String outputExtension, final String indexExtension, final boolean createIndex, final boolean createMD5) throws IOException {
    final TestGATKToolWithVariants tool = new TestGATKToolWithVariants();
    // verify lenient==true is honored by writing a bad attribute
    final File outputFile = setupVCFWriter(inputFile, outputExtension, tool, createIndex, createMD5, true);
    try (VariantContextWriter writer = tool.createVCFWriter(outputFile)) {
        // write bad attribute succeed with lenient set
        writeHeaderAndBadVariant(writer);
    }
    final File outFileIndex = new File(outputFile.getAbsolutePath() + indexExtension);
    final File outFileMD5 = new File(outputFile.getAbsolutePath() + ".md5");
    Assert.assertTrue(outputFile.exists(), "No output file was not created");
    Assert.assertEquals(outFileIndex.exists(), createIndex, "The createIndex argument was not honored");
    Assert.assertEquals(outFileMD5.exists(), createMD5, "The createMD5 argument was not honored");
}

Example 82 with VariantContextWriter

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

the class GATKToolUnitTest method testCreateVCFWriterWithNoSequenceDictionary.

@Test(dataProvider = "createVCFWriterData")
public void testCreateVCFWriterWithNoSequenceDictionary(final File inputFile, final String outputExtension, final String indexExtension, final boolean createIndex, final boolean createMD5) throws IOException {
    // verify that a null sequence dictionary still results in a file, but with no index
    final TestGATKVariantToolWithNoSequenceDictionary tool = new TestGATKVariantToolWithNoSequenceDictionary();
    final File outputFile = setupVCFWriter(inputFile, outputExtension, tool, createIndex, createMD5, false);
    final VariantContextWriter writer = tool.createVCFWriter(outputFile);
    writer.close();
    final File outFileIndex = new File(outputFile.getAbsolutePath() + indexExtension);
    final File outFileMD5 = new File(outputFile.getAbsolutePath() + ".md5");
    Assert.assertTrue(outputFile.exists(), "No output file was not created");
    // always false with no seq dictionary
    Assert.assertEquals(outFileIndex.exists(), false, "An index file should not have been created");
    Assert.assertEquals(outFileMD5.exists(), createMD5, "The createMD5 argument was not honored");
}

Example 83 with VariantContextWriter

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

the class GATKToolUnitTest method testCreateVCFWriterDefaults.

@Test(dataProvider = "createVCFWriterData")
public void testCreateVCFWriterDefaults(// unused
final File inputFile, final String outputExtension, final String indexExtension, // unused
final boolean createIndex, // unused
final boolean createMD5) throws IOException {
    // create a writer and make sure the default index/md5 params are honored
    final TestGATKToolWithVariants tool = createTestVariantTool(null);
    final File tmpDir = createTempDir("createVCFTest");
    final File outputFile = new File(tmpDir.getAbsolutePath(), "createVCFTest" + outputExtension);
    final VariantContextWriter writer = tool.createVCFWriter(outputFile);
    writer.close();
    final File outFileIndex = new File(outputFile.getAbsolutePath() + indexExtension);
    final File outFileMD5 = new File(outputFile.getAbsolutePath() + ".md5");
    Assert.assertTrue(outputFile.exists(), "No output file was not created");
    Assert.assertTrue(outFileIndex.exists(), "The index file was not created");
    Assert.assertFalse(outFileMD5.exists(), "An md5 file was created and should not have been");
}

Example 84 with VariantContextWriter

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

the class SVVCFWriter method writeVariants.

private static void writeVariants(final PipelineOptions pipelineOptions, final String fileName, final List<VariantContext> variantsArrayList, final SAMSequenceDictionary referenceSequenceDictionary) {
    try (final OutputStream outputStream = new BufferedOutputStream(BucketUtils.createFile(fileName))) {
        final VariantContextWriter vcfWriter = getVariantContextWriter(outputStream, referenceSequenceDictionary);
        vcfWriter.writeHeader(getVcfHeader(referenceSequenceDictionary));
        variantsArrayList.forEach(vcfWriter::add);
        vcfWriter.close();
    } catch (final IOException e) {
        throw new GATKException("Could not create output file", e);
    }
}

Example 85 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project hmftools by hartwigmedical.

the class MNVValidatorApplication method processVariants.

private static void processVariants(@NotNull final String filePath, @NotNull final String outputVcf, @NotNull final String tumorBam) {
    final VCFFileReader vcfReader = new VCFFileReader(new File(filePath), false);
    final VariantContextWriter vcfWriter = new VariantContextWriterBuilder().setOutputFile(outputVcf).setReferenceDictionary(vcfReader.getFileHeader().getSequenceDictionary()).build();
    vcfWriter.writeHeader(vcfReader.getFileHeader());
    final MNVValidator validator = ImmutableMNVValidator.of(tumorBam);
    Pair<PotentialMNVRegion, Optional<PotentialMNVRegion>> outputPair = ImmutablePair.of(PotentialMNVRegion.empty(), Optional.empty());
    for (final VariantContext variant : vcfReader) {
        final PotentialMNVRegion potentialMNV = outputPair.getLeft();
        outputPair = MNVDetector.fitsMNVRegion(potentialMNV, variant);
        outputPair.getRight().ifPresent(mnvRegion -> validator.mergeVariants(mnvRegion).forEach(vcfWriter::add));
    }
    validator.mergeVariants(outputPair.getLeft()).forEach(vcfWriter::add);
    vcfWriter.close();
    vcfReader.close();
    LOGGER.info("Written output variants to " + outputVcf);
}