protected VariantContextWriter createVariantContextWriter(Configuration conf, OutputStream out) { return new VariantContextWriterBuilder().clearOptions() .setOutputStream(out).build(); }
protected VariantContextWriter createVariantContextWriter(Configuration conf, OutputStream out) { return new VariantContextWriterBuilder().clearOptions() .setOutputStream(out).build(); }
@Test public void testClearOptions() { // Verify that clearOptions doesn't have a side effect of carrying previously set options // forward to subsequent builders VariantContextWriterBuilder vcwb = new VariantContextWriterBuilder(); vcwb.clearOptions().setOption(Options.INDEX_ON_THE_FLY); final VariantContextWriterBuilder builder = new VariantContextWriterBuilder().clearOptions(); Assert.assertTrue(builder.options.isEmpty()); }
headerOut = out; VariantContextWriter writer = new VariantContextWriterBuilder().clearOptions() .setOutputVCFStream(headerOut).build(); writer.writeHeader(header);
protected VariantContextWriter createVariantContextWriter(Configuration conf, OutputStream out) { return new VariantContextWriterBuilder().clearOptions() .setOption(Options.FORCE_BCF) .setOutputBCFStream(out).build(); }
headerOut = out; VariantContextWriter writer = new VariantContextWriterBuilder().clearOptions() .setOutputVCFStream(headerOut).build(); writer.writeHeader(header);
protected VariantContextWriter createVariantContextWriter(Configuration conf, OutputStream out) { return new VariantContextWriterBuilder().clearOptions() .setOption(Options.FORCE_BCF) .setOutputBCFStream(out).build(); }
headerOut = out; VariantContextWriter writer = new VariantContextWriterBuilder().clearOptions() .setOutputVCFStream(headerOut).build(); writer.writeHeader(header);
private void init( OutputStream output, VCFHeader header, boolean writeHeader) throws IOException { final StoppableOutputStream stopOut = new StoppableOutputStream(!writeHeader, output); writer = new VariantContextWriterBuilder().clearOptions() .setOutputStream(stopOut).build(); writer.writeHeader(header); stopOut.stopped = false; setInputHeader(header); }
@Test public void testStdOut() { final VariantContextWriter writer = new VariantContextWriterBuilder().setOutputFile("/dev/stdout").clearOptions().build(); OutputStream s = ((VCFWriter) writer).getOutputStream(); Assert.assertNotNull(((VCFWriter) writer).getOutputStream()); Assert.assertNotEquals(((VCFWriter) writer).getStreamName(), IndexingVariantContextWriter.DEFAULT_READER_NAME); }
@Test public void testModifyOption() { final VariantContextWriterBuilder builder = new VariantContextWriterBuilder().clearOptions(); for (final Options option : Options.values()) { Assert.assertFalse(builder.isOptionSet(option)); // shouldn't be set builder.modifyOption(option, false); Assert.assertFalse(builder.isOptionSet(option)); // still shouldn't be set builder.modifyOption(option, true); Assert.assertTrue(builder.isOptionSet(option)); // now is set builder.modifyOption(option, false); Assert.assertFalse(builder.isOptionSet(option)); // has been unset } }
public VariantContextWriterBuilder getVariantContextWriterBuilder(File output, boolean createIndex) { VariantContextWriterBuilder builder = new VariantContextWriterBuilder() .setOutputFile(output) .setReferenceDictionary(getReference().getSequenceDictionary()); builder.clearOptions(); if (createIndex) { builder.setOption(Options.INDEX_ON_THE_FLY); } else { builder.clearIndexCreator(); } return builder; } /**
private void init( OutputStream output, VCFHeader header, final boolean writeHeader) throws IOException { final BCFStoppableOutputStream stopOut = new BCFStoppableOutputStream(!writeHeader, output); writer = new VariantContextWriterBuilder().clearOptions() .setOption(Options.FORCE_BCF) .setOutputBCFStream(stopOut).build(); writer.writeHeader(header); stopOut.stopped = false; setInputHeader(header); }
/** * Converts a list of variants into a VCF file, given a {@link VCFHeader} * and an {@link OutputStream}. * <p> This function uses HTSJDK to create {@link VariantCall} objects then * writes them to the given output stream. Note that this implementation depends * heavily on HTSJDK and makes the same assumptions as HTSJDK (e.g. integer values GQ). * * @param header The header to use to generate the output VCF * @param variants A list of variants to encode in the output VCF * @param os The output stream to which to write the generated VCF */ public static void convertVariantToVcf(VCFHeader header, List<Variant> variants, OutputStream os, boolean writeHeader) { if (vcfWriter == null) { vcfWriter = new VariantContextWriterBuilder().clearOptions() .setOutputVCFStream(os).build(); } if (writeHeader) { vcfWriter.writeHeader(header); } for (Variant currVariant : variants) { vcfWriter.add(getContextFromVariant(header, currVariant)); } } }
private void innerWriteToFifo(String pathToFifo) { // Do not enable INDEX_OF_THE_FLY because that is not compatible with writing to a pipe. final VariantContextWriterBuilder builder = new VariantContextWriterBuilder() .clearOptions() .setReferenceDictionary(dictionary); Path vcfPath = Paths.get(pathToFifo); VariantContextWriter writer = builder.setOutputPath(vcfPath).build(); writer.writeHeader(new VCFHeader()); writer.close(); }
.clearOptions(); if (CREATE_INDEX) builder.setOption(Options.INDEX_ON_THE_FLY);
.clearOptions(); if (CREATE_INDEX) builder.setOption(Options.INDEX_ON_THE_FLY);
.clearOptions(); if (CREATE_INDEX) builder.setOption(Options.INDEX_ON_THE_FLY);
.clearOptions(); if (CREATE_INDEX) builder.setOption(Options.INDEX_ON_THE_FLY);