@Test public void testVCFHeaderSerialization() throws Exception { final VCFFileReader reader = new VCFFileReader(new File("testdata/htsjdk/variant/HiSeq.10000.vcf"), false); final VCFHeader originalHeader = reader.getFileHeader(); reader.close(); final VCFHeader deserializedHeader = TestUtil.serializeAndDeserialize(originalHeader); Assert.assertEquals( deserializedHeader.getMetaDataInInputOrder(), originalHeader.getMetaDataInInputOrder(), "Header metadata does not match before/after serialization"); Assert.assertEquals( deserializedHeader.getContigLines(), originalHeader.getContigLines(), "Contig header lines do not match before/after serialization"); Assert.assertEquals( deserializedHeader.getFilterLines(), originalHeader.getFilterLines(), "Filter header lines do not match before/after serialization"); Assert.assertEquals( deserializedHeader.getFormatHeaderLines(), originalHeader.getFormatHeaderLines(), "Format header lines do not match before/after serialization"); Assert.assertEquals( deserializedHeader.getIDHeaderLines(), originalHeader.getIDHeaderLines(), "ID header lines do not match before/after serialization"); Assert.assertEquals( deserializedHeader.getInfoHeaderLines(), originalHeader.getInfoHeaderLines(), "Info header lines do not match before/after serialization"); Assert.assertEquals( deserializedHeader.getOtherHeaderLines(), originalHeader.getOtherHeaderLines(), "Other header lines do not match before/after serialization"); Assert.assertEquals( deserializedHeader.getGenotypeSamples(), originalHeader.getGenotypeSamples(), "Genotype samples not the same before/after serialization"); Assert.assertEquals( deserializedHeader.samplesWereAlreadySorted(), originalHeader.samplesWereAlreadySorted(), "Sortedness of samples not the same before/after serialization"); Assert.assertEquals( deserializedHeader.getSampleNamesInOrder(), originalHeader.getSampleNamesInOrder(), "Sorted list of sample names in header not the same before/after serialization"); Assert.assertEquals( deserializedHeader.getSampleNameToOffset(), originalHeader.getSampleNameToOffset(), "Sample name to offset map not the same before/after serialization"); Assert.assertEquals( deserializedHeader.toString(), originalHeader.toString(), "String representation of header not the same before/after serialization"); }