public boolean hasFormatLine(final String id) { return getFormatHeaderLine(id) != null; }
@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"); }
public boolean hasFormatLine(final String id) { return getFormatHeaderLine(id) != null; }
public boolean hasFormatLine(final String id) { return getFormatHeaderLine(id) != null; }
public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) { VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field); if ( metaData == null ) metaData = header.getInfoHeaderLine(field); if ( metaData == null ) { if ( ASSUME_MISSING_FIELDS_ARE_STRINGS ) { if ( ! MISSING_KEYS_WARNED_ABOUT.contains(field) ) { MISSING_KEYS_WARNED_ABOUT.add(field); if ( GeneralUtils.DEBUG_MODE_ENABLED ) System.err.println("Field " + field + " missing from VCF header, assuming it is an unbounded string type"); } return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field); } else throw new TribbleException("Fully decoding VariantContext requires header line for all fields, but none was found for " + field); } return metaData; }
public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) { VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field); if ( metaData == null ) metaData = header.getInfoHeaderLine(field); if ( metaData == null ) { if ( ASSUME_MISSING_FIELDS_ARE_STRINGS ) { if ( ! MISSING_KEYS_WARNED_ABOUT.contains(field) ) { MISSING_KEYS_WARNED_ABOUT.add(field); if ( GeneralUtils.DEBUG_MODE_ENABLED ) System.err.println("Field " + field + " missing from VCF header, assuming it is an unbounded string type"); } return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field); } else throw new TribbleException("Fully decoding VariantContext requires header line for all fields, but none was found for " + field); } return metaData; }
private void loadVCF(ResourceLocator locator, List<Track> newTracks, Genome genome) throws IOException, TribbleIndexNotFoundException { TribbleFeatureSource src = TribbleFeatureSource.getFeatureSource(locator, genome); VCFHeader header = (VCFHeader) src.getHeader(); // Test if the input VCF file contains methylation rate data: // This is determined by testing for the presence of two sample format fields: MR and GB, used in the // rendering of methylation rate. // MR is the methylation rate on a scale of 0 to 100% and GB is the number of bases that pass // filter for the position. GB is needed to avoid displaying positions for which limited coverage // prevents reliable estimation of methylation rate. boolean enableMethylationRateSupport = (header.getFormatHeaderLine("MR") != null && header.getFormatHeaderLine("GB") != null); List<String> allSamples = new ArrayList(header.getGenotypeSamples()); VariantTrack t = new VariantTrack(locator, src, allSamples, enableMethylationRateSupport); // VCF tracks handle their own margin t.setMargin(0); newTracks.add(t); }
public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) { VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field); if ( metaData == null ) metaData = header.getInfoHeaderLine(field); if ( metaData == null ) { if ( ASSUME_MISSING_FIELDS_ARE_STRINGS ) { if ( ! MISSING_KEYS_WARNED_ABOUT.contains(field) ) { MISSING_KEYS_WARNED_ABOUT.add(field); if ( GeneralUtils.DEBUG_MODE_ENABLED ) System.err.println("Field " + field + " missing from VCF header, assuming it is an unbounded string type"); } return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field); } else throw new TribbleException("Fully decoding VariantContext requires header line for all fields, but none was found for " + field); } return metaData; }
private void loadVCFListFile(ResourceLocator locator, List<Track> newTracks, Genome genome) throws IOException, TribbleIndexNotFoundException { TribbleListFeatureSource src = new TribbleListFeatureSource(locator.getPath(), genome); VCFHeader header = (VCFHeader) src.getHeader(); // Test if the input VCF file contains methylation rate data: // This is determined by testing for the presence of two sample format fields: MR and GB, used in the // rendering of methylation rate. // MR is the methylation rate on a scale of 0 to 100% and GB is the number of bases that pass // filter for the position. GB is needed to avoid displaying positions for which limited coverage // prevents reliable estimation of methylation rate. boolean enableMethylationRateSupport = (header.getFormatHeaderLine("MR") != null && header.getFormatHeaderLine("GB") != null); List<String> allSamples = new ArrayList(header.getGenotypeSamples()); VariantTrack t = new VariantTrack(locator, src, allSamples, enableMethylationRateSupport); // VCF tracks handle their own margin t.setMargin(0); newTracks.add(t); }
if(tag.trim().startsWith("FMT/") || track.getVcfHeader().getFormatHeaderLine(tag) != null){ fname= "getFmtTag";
final VCFFormatHeaderLine metaData = header.getFormatHeaderLine(field); if (metaData == null) { logger.log(Level.WARNING, String.format("Could not find matching VCF header field for "
Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4; final VCFFormatHeaderLine metaData = this.header.getFormatHeaderLine(field); if (metaData != null) { final int numInFormatField = metaData.getCount(vc);
Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4; final VCFFormatHeaderLine metaData = this.header.getFormatHeaderLine(field); if (metaData != null) { final int numInFormatField = metaData.getCount(vc);
if (header.getFormatHeaderLine(id) == null) { header.addMetaDataLine(new VCFFormatHeaderLine(id, 1, VCFHeaderLineType.valueOf(line.getType()), ""));
VCFHeaderLineType type = header.getFormatHeaderLine(currKey).getType(); if (currSize == 1) { attributes.put(currKey, parseObject(currKey, currValue.get(0), type));
Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4; final VCFFormatHeaderLine metaData = this.header.getFormatHeaderLine(field); if ( metaData != null ) { final int numInFormatField = metaData.getCount(vc);
@Test(dataProvider = "RepairHeaderTest") public void testRepairHeaderTest(final RepairHeaderTest cfg) { final VCFHeader toRepair = new VCFHeader(Collections.singleton((VCFHeaderLine)cfg.original)); final VCFHeader repaired = VCFStandardHeaderLines.repairStandardHeaderLines(toRepair); VCFCompoundHeaderLine repairedLine = (VCFCompoundHeaderLine)repaired.getFormatHeaderLine(cfg.original.getID()); if ( repairedLine == null ) repairedLine = (VCFCompoundHeaderLine)repaired.getInfoHeaderLine(cfg.original.getID()); Assert.assertNotNull(repairedLine, "Repaired header didn't contain the expected line"); Assert.assertEquals(repairedLine.getID(), cfg.expectedResult.getID()); Assert.assertEquals(repairedLine.getType(), cfg.expectedResult.getType()); Assert.assertEquals(repairedLine.getCountType(), cfg.expectedResult.getCountType()); if ( repairedLine.getCountType() == VCFHeaderLineCount.INTEGER ) { Assert.assertEquals(repairedLine.getCount(), cfg.expectedResult.getCount()); } } }