@Test public void test() { FullVcfCodec fc = new FullVcfCodec(); fc.setVCFHeader(this.header, this.version); VariantContextBlockIterator iter = new VariantContextBlockIterator(fc); List<VariantContext> ctxList = iter.convert(this.rows); assertEquals("Assume the same list size", this.rows.size(), ctxList.size()); }
/** @throws java.lang.Exception */ @Before public void setUp() throws Exception { rows = new LinkedList<CharBuffer>(); String inFile = "/" + this.getClass().getName().replaceAll("\\.", "/") + ".vcf"; FullVcfCodec codec = new FullVcfCodec(); try (InputStream in = getStream(inFile); ) { LineIterator iter = codec.makeSourceFromStream(in); this.header = (VCFHeader) codec.readActualHeader(iter); this.version = codec.getVCFHeaderVersion(); } try (InputStream in = getStream(inFile); ) { List<String> lines = IOUtils.readLines(in); for (String l : lines) { if (!l.startsWith("#")) { rows.add(CharBuffer.wrap(l)); } } } // rows.add(CharBuffer.wrap("20 60479 rs149529999 C T 100 PASS // ERATE=0.0005;RSQ=0.8951;LDAF=0.0021; GT:DS:GL 0|0:0.000:-0.19,-0.46,-2.68 // 0|0:0.000:-0.01,-1.85,-5.00")); }