@Test public void testVCFHeaderAddContigLine() { final VCFHeader header = getHiSeqVCFHeader(); final VCFContigHeaderLine contigLine = new VCFContigHeaderLine( "<ID=chr1,length=1234567890,assembly=FAKE,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=\"Homo sapiens\">", VCFHeaderVersion.VCF4_0, VCFHeader.CONTIG_KEY, 0); header.addMetaDataLine(contigLine); Assert.assertTrue(header.getContigLines().contains(contigLine), "Test contig line not found in contig header lines"); Assert.assertTrue(header.getMetaDataInInputOrder().contains(contigLine), "Test contig line not found in set of all header lines"); Assert.assertFalse(header.getInfoHeaderLines().contains(contigLine), "Test contig line present in info header lines"); Assert.assertFalse(header.getFormatHeaderLines().contains(contigLine), "Test contig line present in format header lines"); Assert.assertFalse(header.getFilterLines().contains(contigLine), "Test contig line present in filter header lines"); Assert.assertFalse(header.getOtherHeaderLines().contains(contigLine), "Test contig line present in other header lines"); }
@Test public void testVCFHeaderAddDuplicateHeaderLine() { File input = new File("src/test/resources/htsjdk/variant/ex2.vcf"); VCFFileReader reader = new VCFFileReader(input, false); VCFHeader header = reader.getFileHeader(); VCFHeaderLine newHeaderLine = new VCFHeaderLine("key", "value"); // add this new header line header.addMetaDataLine(newHeaderLine); final int numHeaderLinesBefore = header.getOtherHeaderLines().size(); // readd the same header line header.addMetaDataLine(newHeaderLine); final int numHeaderLinesAfter = header.getOtherHeaderLines().size(); // assert that we have the same number of other header lines before and after Assert.assertEquals(numHeaderLinesBefore, numHeaderLinesAfter); }
@Test public void testVCFHeaderAddOtherLine() { final VCFHeader header = getHiSeqVCFHeader(); final VCFHeaderLine otherLine = new VCFHeaderLine("TestOtherLine", "val"); header.addMetaDataLine(otherLine); Assert.assertTrue(header.getOtherHeaderLines().contains(otherLine), "TestOtherLine not found in other header lines"); Assert.assertTrue(header.getMetaDataInInputOrder().contains(otherLine), "TestOtherLine not found in set of all header lines"); Assert.assertNotNull(header.getOtherHeaderLine("TestOtherLine"), "Lookup for TestOtherLine by key failed"); Assert.assertFalse(header.getInfoHeaderLines().contains(otherLine), "TestOtherLine present in info header lines"); Assert.assertFalse(header.getFormatHeaderLines().contains(otherLine), "TestOtherLine present in format header lines"); Assert.assertFalse(header.getContigLines().contains(otherLine), "TestOtherLine present in contig header lines"); Assert.assertFalse(header.getFilterLines().contains(otherLine), "TestOtherLine present in filter header lines"); }
@Test public void testVCFHeaderAddInfoLine() { final VCFHeader header = getHiSeqVCFHeader(); final VCFInfoHeaderLine infoLine = new VCFInfoHeaderLine("TestInfoLine", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "test info line"); header.addMetaDataLine(infoLine); Assert.assertTrue(header.getInfoHeaderLines().contains(infoLine), "TestInfoLine not found in info header lines"); Assert.assertTrue(header.getMetaDataInInputOrder().contains(infoLine), "TestInfoLine not found in set of all header lines"); Assert.assertNotNull(header.getInfoHeaderLine("TestInfoLine"), "Lookup for TestInfoLine by key failed"); Assert.assertFalse(header.getFormatHeaderLines().contains(infoLine), "TestInfoLine present in format header lines"); Assert.assertFalse(header.getFilterLines().contains(infoLine), "TestInfoLine present in filter header lines"); Assert.assertFalse(header.getContigLines().contains(infoLine), "TestInfoLine present in contig header lines"); Assert.assertFalse(header.getOtherHeaderLines().contains(infoLine), "TestInfoLine present in other header lines"); }
@Test public void testVCFHeaderAddFormatLine() { final VCFHeader header = getHiSeqVCFHeader(); final VCFFormatHeaderLine formatLine = new VCFFormatHeaderLine("TestFormatLine", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "test format line"); header.addMetaDataLine(formatLine); Assert.assertTrue(header.getFormatHeaderLines().contains(formatLine), "TestFormatLine not found in format header lines"); Assert.assertTrue(header.getMetaDataInInputOrder().contains(formatLine), "TestFormatLine not found in set of all header lines"); Assert.assertNotNull(header.getFormatHeaderLine("TestFormatLine"), "Lookup for TestFormatLine by key failed"); Assert.assertFalse(header.getInfoHeaderLines().contains(formatLine), "TestFormatLine present in info header lines"); Assert.assertFalse(header.getFilterLines().contains(formatLine), "TestFormatLine present in filter header lines"); Assert.assertFalse(header.getContigLines().contains(formatLine), "TestFormatLine present in contig header lines"); Assert.assertFalse(header.getOtherHeaderLines().contains(formatLine), "TestFormatLine present in other header lines"); }
@Test public void testVCFHeaderAddFilterLine() { final VCFHeader header = getHiSeqVCFHeader(); final String filterDesc = "TestFilterLine Description"; final VCFFilterHeaderLine filterLine = new VCFFilterHeaderLine("TestFilterLine",filterDesc); Assert.assertEquals(filterDesc,filterLine.getDescription()); header.addMetaDataLine(filterLine); Assert.assertTrue(header.getFilterLines().contains(filterLine), "TestFilterLine not found in filter header lines"); Assert.assertTrue(header.getMetaDataInInputOrder().contains(filterLine), "TestFilterLine not found in set of all header lines"); Assert.assertNotNull(header.getFilterHeaderLine("TestFilterLine"), "Lookup for TestFilterLine by key failed"); Assert.assertFalse(header.getInfoHeaderLines().contains(filterLine), "TestFilterLine present in info header lines"); Assert.assertFalse(header.getFormatHeaderLines().contains(filterLine), "TestFilterLine present in format header lines"); Assert.assertFalse(header.getContigLines().contains(filterLine), "TestFilterLine present in contig header lines"); Assert.assertFalse(header.getOtherHeaderLines().contains(filterLine), "TestFilterLine present in other header lines"); }
@Test public void testVCFHeaderSerialization() throws Exception { final VCFFileReader reader = new VCFFileReader(new File("src/test/resources/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"); }