@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"));
}