vc.set(v, header);
vc.set(v, header);
@Override public boolean nextKeyValue() throws IOException { while (true) { String line; while (true) { if (!lineRecordReader.nextKeyValue()) { return false; } line = lineRecordReader.getCurrentValue().toString(); if (!line.startsWith("#")) { break; } } final VariantContext v = codec.decode(line); if (!overlaps(v)) { continue; } Integer chromIdx = contigDict.get(v.getContig()); if (chromIdx == null) chromIdx = (int) MurmurHash3.murmurhash3(v.getContig(), 0); key.set((long) chromIdx << 32 | (long) (v.getStart() - 1)); vc.set(v, header); return true; } }
@Override public boolean nextKeyValue() throws IOException { if (in.peek() == -1) return false; if (!isBGZF && in.getPosition() >= fileStart + length) return false; final VariantContext v = codec.decode(in); Integer chromIdx = contigDict.get(v.getContig()); if (chromIdx == null) chromIdx = (int)MurmurHash3.murmurhash3(v.getContig(), 0); key.set((long)chromIdx << 32 | (long)(v.getStart() - 1)); vc.set(v); return true; } }
@Override public boolean nextKeyValue() throws IOException { if (in.peek() == -1) return false; if (!isBGZF && in.getPosition() >= fileStart + length) return false; final VariantContext v = codec.decode(in); Integer chromIdx = contigDict.get(v.getContig()); if (chromIdx == null) chromIdx = (int)MurmurHash3.murmurhash3(v.getContig(), 0); key.set((long)chromIdx << 32 | (long)(v.getStart() - 1)); vc.set(v); return true; } }
@Override public boolean nextKeyValue() throws IOException { if (in.peek() == -1) return false; if (!isBGZF && in.getPosition() >= fileStart + length) return false; final VariantContext v = codec.decode(in); Integer chromIdx = contigDict.get(v.getContig()); if (chromIdx == null) chromIdx = (int)MurmurHash3.murmurhash3(v.getContig(), 0); key.set((long)chromIdx << 32 | (long)(v.getStart() - 1)); vc.set(v); return true; } }
@Test public void testSimple() throws Exception { VariantContextBuilder vctx_builder = new VariantContextBuilder(); ArrayList<Allele> alleles = new ArrayList<Allele>(); alleles.add(Allele.create("A", false)); alleles.add(Allele.create("C", true)); vctx_builder.alleles(alleles); GenotypesContext genotypes = GenotypesContext.NO_GENOTYPES; vctx_builder.genotypes(genotypes); HashSet<String> filters = new HashSet<String>(); vctx_builder.filters(filters); HashMap<String, Object> attributes = new HashMap<String, Object>(); attributes.put("NS", new Integer(4)); vctx_builder.attributes(attributes); vctx_builder.loc("20", 2, 2); vctx_builder.log10PError(-8.0); String[] expected = new String[]{"20", "2", ".", "C", "A", "80", "PASS", "NS=4"}; VariantContext ctx = vctx_builder.make(); writable.set(ctx); writer.write(1L, writable); writer.close(taskAttemptContext); LineNumberReader reader = new LineNumberReader(new FileReader(test_vcf_output)); skipHeader(reader); String[] fields = Arrays.copyOf(reader.readLine().split("\t"), expected.length); Assert.assertArrayEquals("comparing VCF single line", expected, fields); }
writable.set(ctxh);