public boolean hasFilterLine(final String id) { return getFilterHeaderLine(id) != null; }
public boolean hasFilterLine(final String id) { return getFilterHeaderLine(id) != null; }
public boolean hasFilterLine(final String id) { return getFilterHeaderLine(id) != null; }
@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"); }
originalHeader.addMetaDataLine(addedHeaderLine); final VCFFilterHeaderLine originalCopyAnnotationLine1 = originalHeader.getFilterHeaderLine("ANNOTATION"); Assert.assertNotNull(originalCopyAnnotationLine1); Assert.assertEquals(originalCopyAnnotationLine1.getGenericFieldValue("Description"), "ANNOTATION != \"NA\" || ANNOTATION <= 0.01", originalCopyAnnotationLine1.toString()); final VCFFilterHeaderLine originalCopyAnnotationLine2 = originalHeader.getFilterHeaderLine("ANNOTATION2"); Assert.assertNotNull(originalCopyAnnotationLine2); Assert.assertEquals(originalCopyAnnotationLine2.getGenericFieldValue("Description"), "ANNOTATION with quote \" that is unmatched but escaped"); Assert.assertNotNull(firstCopyNewHeaderLine); final VCFFilterHeaderLine firstCopyAnnotationLine1 = firstCopyHeader.getFilterHeaderLine("ANNOTATION"); Assert.assertNotNull(firstCopyAnnotationLine1); Assert.assertEquals(firstCopyAnnotationLine1.getGenericFieldValue("Description"), "ANNOTATION != \"NA\" || ANNOTATION <= 0.01"); final VCFFilterHeaderLine firstCopyAnnotationLine2 = firstCopyHeader.getFilterHeaderLine("ANNOTATION2"); Assert.assertNotNull(firstCopyAnnotationLine2); Assert.assertNotNull(secondCopyNewHeaderLine); final VCFFilterHeaderLine secondCopyAnnotationLine1 = secondCopyHeader.getFilterHeaderLine("ANNOTATION"); Assert.assertNotNull(secondCopyAnnotationLine1); final VCFFilterHeaderLine secondCopyAnnotationLine2 = secondCopyHeader.getFilterHeaderLine("ANNOTATION2"); Assert.assertNotNull(secondCopyAnnotationLine2);