@Test
public void testVCFHeaderSampleRenamingSingleSampleVCF() throws Exception {
final VCFCodec codec = new VCFCodec();
codec.setRemappedSampleName("FOOSAMPLE");
final AsciiLineReaderIterator vcfIterator = new AsciiLineReaderIterator(AsciiLineReader.from(new FileInputStream(variantTestDataRoot + "HiSeq.10000.vcf")));
final VCFHeader header = (VCFHeader) codec.readHeader(vcfIterator).getHeaderValue();
Assert.assertEquals(header.getNGenotypeSamples(), 1, "Wrong number of samples in remapped header");
Assert.assertEquals(header.getGenotypeSamples().get(0), "FOOSAMPLE", "Sample name in remapped header has incorrect value");
int recordCount = 0;
while (vcfIterator.hasNext() && recordCount < 10) {
recordCount++;
final VariantContext vcfRecord = codec.decode(vcfIterator.next());
Assert.assertEquals(vcfRecord.getSampleNames().size(), 1, "Wrong number of samples in vcf record after remapping");
Assert.assertEquals(vcfRecord.getSampleNames().iterator().next(), "FOOSAMPLE", "Wrong sample in vcf record after remapping");
}
}