public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) { return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString()); }
public Map<String, Object> annotate(final RefMetaDataTracker tracker, final AnnotatorCompatible walker, final ReferenceContext ref, final Map<String, AlignmentContext> stratifiedContexts, final VariantContext vc, final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) { StringBuffer type = new StringBuffer(""); if ( vc.isVariant() && !vc.isBiallelic() ) type.append("MULTIALLELIC_"); if ( !vc.isIndel() ) { type.append(vc.getType().toString()); } else { if (vc.isSimpleInsertion()) type.append("INSERTION."); else if (vc.isSimpleDeletion()) type.append("DELETION."); else type.append("COMPLEX."); ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref); type.append(IndelUtils.getIndelClassificationName(inds.get(0))); for (int i = 1; i < inds.size(); i++ ) { type.append("."); type.append(IndelUtils.getIndelClassificationName(inds.get(i))); } } Map<String, Object> map = new HashMap<>(); map.put(getKeyNames().get(0), String.format("%s", type)); return map; }
@Override public void initialize() { for (VariantContext.Type t : VariantContext.Type.values()) states.add(t.toString()); }
variant.setType(getEnumFromString(VariantProto.VariantType.class, variantContext.getType().toString()));
infoMap.put("TYPE", vc.getType().toString()); infoMap.put("QUAL", String.valueOf(vc.getPhredScaledQual()));
private static Object splitAlleleTypes(VariantContext vc) { final int numAltAlleles = vc.getAlternateAlleles().size(); if (numAltAlleles == 1) return vc.getType().toString(); List<Allele> altAlleles = vc.getAlternateAlleles(); List<String> alleleTypes = new ArrayList<>(numAltAlleles); for (Allele allele : altAlleles) { if (allele.length() == vc.getReference().length()) { if ( allele.length() == 1 ) alleleTypes.add("SNP"); else alleleTypes.add("MNP"); } else alleleTypes.add("INDEL"); } return alleleTypes; } }
x.put("TYPE", new AttributeGetter() { public Object get(VariantContext vc) { return vc.getType().toString(); }}); x.put("QUAL", new AttributeGetter() { public Object get(VariantContext vc) { return -10 * vc.getLog10PError(); }});
getters.put("TYPE", new Getter() { public String get(VariantContext vc) { return vc.getType().toString(); } }); getters.put("VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount() + vc.getHomVarCount()); } });
public String getType() { return variantContext.getType().toString(); }
private VCFVariant tstStart(String chr, int fileFeatStart, VariantContext.Type variantType, int expFeatStart) throws Exception{ VCFVariant variant = get_hc_mod_Feat(chr, fileFeatStart - 5, fileFeatStart + 5); assertEquals(variantType.toString(), variant.getType()); assertEquals(expFeatStart, variant.getStart()); return variant; } }