@Override public Feature decodeLoc( final PositionalBufferedStream inputStream ) { return decode(inputStream); }
@Override public Feature decodeLoc( final PositionalBufferedStream inputStream ) { return decode(inputStream); }
@Override public Feature decodeLoc( final PositionalBufferedStream inputStream ) { return decode(inputStream); }
@Override protected VariantContext advance() { return this.codec.isDone(this.inputStream) ? null : this.codec.decode(this.inputStream); }
@Override protected VariantContext advance() { return this.codec.isDone(this.inputStream) ? null : this.codec.decode(this.inputStream); }
@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; } }
VariantContext vc = codec.decode(headerPbs); Assert.assertEquals(vc.getGenotypes().stream().filter(Genotype::isPhased).count(), 2); vcfWriter.add(vc);
VariantContext vc = codec.decode(bodyPbs); counter++;