Java VariantContextWriter.close方法代码示例

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
private static void processVariants(@NotNull final String filePath, @NotNull final Slicer highConfidenceSlicer,
        @NotNull final String outputVcf, @NotNull final String sampleName, @NotNull final String tumorBam) throws HartwigException {
    final VCFFileReader vcfReader = new VCFFileReader(new File(filePath), false);
    final VCFHeader outputHeader = generateOutputHeader(vcfReader.getFileHeader(), sampleName);
    final VariantContextWriter writer = new VariantContextWriterBuilder().setOutputFile(outputVcf)
            .setReferenceDictionary(outputHeader.getSequenceDictionary())
            .build();
    writer.writeHeader(outputHeader);
    final MNVValidator validator = ImmutableMNVValidator.of(tumorBam);
    Pair<PotentialMNVRegion, Optional<PotentialMNVRegion>> outputPair = ImmutablePair.of(PotentialMNVRegion.empty(), Optional.empty());

    final VariantContextFilter filter = new StrelkaPostProcess(highConfidenceSlicer);
    for (final VariantContext variantContext : vcfReader) {
        if (filter.test(variantContext)) {
            final VariantContext simplifiedVariant = StrelkaPostProcess.simplifyVariant(variantContext, sampleName);
            final PotentialMNVRegion potentialMNV = outputPair.getLeft();
            outputPair = MNVDetector.fitsMNVRegion(potentialMNV, simplifiedVariant);
            outputPair.getRight().ifPresent(mnvRegion -> validator.mergeVariants(mnvRegion).forEach(writer::add));
        }
    }
    validator.mergeVariants(outputPair.getLeft()).forEach(writer::add);
    writer.close();
    vcfReader.close();
    LOGGER.info("Written output variants to " + outputVcf);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
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);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
public static List<String> vcfHeaderToStrings(VCFHeader header) {

	    File fakeVCFFile;
	    List<String> str= new ArrayList<String>();
	    try {
	    	fakeVCFFile = Utils.createTempFile(".vcfheader", ".vcf");
		    fakeVCFFile.deleteOnExit();
			final VariantContextWriter writer = new VariantContextWriterBuilder()
		            .setOutputFile(fakeVCFFile)
		            .setReferenceDictionary(header.getSequenceDictionary())
		            .setOptions(EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Options.WRITE_FULL_FORMAT_FIELD))
		            .build();
		    writer.writeHeader(header);
		    writer.close();
		    BufferedReader br= new BufferedReader(new FileReader(fakeVCFFile));
		    String line= br.readLine();
		    while(line != null){
		    	str.add(line);
		    	line= br.readLine();
		    }
		    br.close();
		} catch (IOException e) {
			e.printStackTrace();
		}
		return str;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
/**
 * This method makes a copy of the input VCF and creates an index file for it in the same location.
 * This is done so that we don't need to store the index file in the same repo
 * The copy of the input is done so that it and its index are in the same directory which is typically required.
 *
 * @param vcfFile the vcf file to index
 * @return File a vcf file (index file is created in same path).
 */
public static File createTemporaryIndexedVcfFromInput(final File vcfFile, final String tempFilePrefix) throws IOException {
    final String extension;

    if (vcfFile.getAbsolutePath().endsWith(".vcf")) extension = ".vcf";
    else if (vcfFile.getAbsolutePath().endsWith(".vcf.gz")) extension = ".vcf.gz";
    else
        throw new IllegalArgumentException("couldn't find a .vcf or .vcf.gz ending for input file " + vcfFile.getAbsolutePath());

    File output = createTemporaryIndexedVcfFile(tempFilePrefix, extension);

    final VCFFileReader in = new VCFFileReader(vcfFile, false);
    final VCFHeader header = in.getFileHeader();

    final VariantContextWriter out = new VariantContextWriterBuilder().
            setReferenceDictionary(header.getSequenceDictionary()).
            setOptions(EnumSet.of(Options.INDEX_ON_THE_FLY)).
            setOutputFile(output).build();
    out.writeHeader(header);
    for (final VariantContext ctx : in) {
        out.add(ctx);
    }
    out.close();
    in.close();
    return output;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Test(dataProvider = "createVCFWriterData")
public void testCreateVCFWriterDefaults(
        final File inputFile,           // unused
        final String outputExtension,
        final String indexExtension,
        final boolean createIndex,      // unused
        final boolean createMD5         // unused
) 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");
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Test(dataProvider = "createVCFWriterData")
public void testCreateVCFWriterWithOptions(
        final File inputFile,
        final String outputExtension,
        final String indexExtension,
        final boolean createIndex,
        final boolean createMD5) throws IOException {

    // create a writer and make sure the requested index/md5 params are honored
    final TestGATKToolWithVariants tool = new TestGATKToolWithVariants();

    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");
    Assert.assertEquals(outFileIndex.exists(), createIndex, "The createIndex argument was not honored");
    Assert.assertEquals(outFileMD5.exists(), createMD5, "The createMD5 argument was not honored");
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@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");
    Assert.assertEquals(outFileIndex.exists(), false, "An index file should not have been created"); // always false with no seq dictionary
    Assert.assertEquals(outFileMD5.exists(), createMD5, "The createMD5 argument was not honored");
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(
	final String inputName,
	final VcfIterator in,
	final VariantContextWriter delegate)
	{
	final VariantContextWriter  out = this.component.open(delegate);
	final SAMSequenceDictionaryProgress progess=new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
	out.writeHeader(in.getHeader());
	while(in.hasNext())
		{
		out.add(progess.watch(in.next()));
		}
	progess.finish();
	out.close();
	return 0;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(final String inputName, final VcfIterator r, final VariantContextWriter delegate) {
	final VariantContextWriter w = this.component.open(delegate);
	w.writeHeader(r.getHeader());
	final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(r.getHeader()).logger(LOG);
	while(r.hasNext())
		{
		w.add(progress.watch(r.next()));
		
		// JVM crash sometimes ? suspect there is a memory leak ?
		if(progress.getCount()%1000L==0)
			{
			System.gc();
			}
		}
	progress.finish();
	w.close();
	return 0;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(
	final String inputName,
	final VcfIterator in,
	final VariantContextWriter delegate)
	{
	final VariantContextWriter  out = this.component.open(delegate);
	final SAMSequenceDictionaryProgress progess=new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
	out.writeHeader(in.getHeader());
	while(in.hasNext() &&  !out.checkError())
		{
		out.add(progess.watch(in.next()));
		}
	progess.finish();
	out.close();
	return 0;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(
		final String inputName,final VcfIterator vcfIterator,
		final VariantContextWriter delegate) {
		final VcfIterator in = VCFUtils.createAssertSortedVcfIterator(vcfIterator, VCFUtils.createTidPosComparator(vcfIterator.getHeader().getSequenceDictionary()));
		final VariantContextWriter out  = this.component.open(delegate);
		
		final SAMSequenceDictionaryProgress progess=new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
		out.writeHeader(in.getHeader());
		while(in.hasNext())
			{
			out.add(progess.watch(in.next()));
			}
		out.close();
		progess.finish();
		CloserUtil.close(in);
		return 0;
		}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(
		final String inputName,
		final VcfIterator iter,
		final VariantContextWriter delegate
		) {	
	final VariantContextWriter out = this.component.open(delegate);
	final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(iter.getHeader()).logger(LOG);
	out.writeHeader(iter.getHeader());
	while(iter.hasNext())
		{
		out.add(progress.watch(iter.next()));
		}
	out.close();
	progress.finish();
	return 0;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(
		final String inputName, 
		final VcfIterator in,
		final VariantContextWriter delegate) {
	
	try
		{
		final VariantContextWriter out  = this.component.open(delegate);
		out.writeHeader(in.getHeader());
		
		final SAMSequenceDictionaryProgress progress= new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
		while(in.hasNext())
			{
			out.add(progress.watch(in.next()));
			}
		progress.finish();
		out.close();
		return 0;
		}
	catch(final Exception err)
		{
		LOG.error(err);
		return -1;
		}
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override
protected int doVcfToVcf(
		final String inputName,
		final VcfIterator r,
		final VariantContextWriter delegate
		) 
	{
	
	final VariantContextWriter w= this.component.open(delegate);

	w.writeHeader(r.getHeader());
	final SAMSequenceDictionaryProgress progress= new SAMSequenceDictionaryProgress(r.getHeader()).logger(LOG);
	while(r.hasNext())
		{
		w.add(progress.watch(r.next()));
		}
	progress.finish();
	w.close();
	return RETURN_OK;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriter; //导入方法依赖的package包/类
@Override 
protected int doVcfToVcf(
		final String inputName, 
		final VcfIterator in,
		final VariantContextWriter delegate) {
	try
		{
		final VariantContextWriter out  = this.component.open(delegate);
		out.writeHeader(in.getHeader());
		final SAMSequenceDictionaryProgress progress= new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
		while(in.hasNext())
			{
			out.add(progress.watch(in.next()));
			}
		progress.finish();
		out.close();
		return 0;
		}
	catch(final Exception err)
		{
		LOG.error(err);
		return -1;
		}
	}