public static VCFHeaderLineType getVCFHeaderLineType(VariantFileHeaderComplexLine line) { if (StringUtils.isEmpty(line.getType())) { return null; } else { return VCFHeaderLineType.valueOf(line.getType()); } }
private VCFHeaderLine convertToFormat(VariantSetMetadata vsm) { String nbr = vsm.getNumber().toString(); VCFHeaderLineCount cl = valueOfLineCountHeader(nbr); VCFFormatHeaderLine hl; if (null != cl) { hl = new VCFFormatHeaderLine(vsm.getId().toString(), cl, VCFHeaderLineType.valueOf(vsm.getType().toString()), vsm.getDescription().toString()); } else { hl = new VCFFormatHeaderLine(vsm.getId().toString(), Integer.valueOf(nbr), VCFHeaderLineType.valueOf(vsm.getType().toString()), vsm.getDescription().toString()); } return hl; }
private VCFInfoHeaderLine convertToInfo(VariantSetMetadata vsm) { String nbr = vsm.getNumber().toString(); VCFHeaderLineCount cl = valueOfLineCountHeader(nbr); VCFInfoHeaderLine hl; if (null != cl) { hl = new VCFInfoHeaderLine(vsm.getId().toString(), cl, VCFHeaderLineType.valueOf(vsm.getType().toString()), vsm.getDescription().toString()); } else { hl = new VCFInfoHeaderLine(vsm.getId().toString(), Integer.valueOf(vsm.getNumber().toString()), VCFHeaderLineType.valueOf(vsm.getType().toString()), vsm.getDescription().toString()); } return hl; }
refAnnotated, ImmutableList.of(fieldName), ImmutableMap.of(fieldName, new GenericTSVValueColumnDescription(colValue, VCFHeaderLineType.valueOf(fieldType), fieldName, fieldDescription, GenericTSVAccumulationStrategy.valueOf(accStrategy))));
type = VCFHeaderLineType.valueOf(mapping.get("Type")); } catch (Exception e) { throw new TribbleException(mapping.get("Type") + " is not a valid type in the VCF specification (note that types are case-sensitive)");
type = VCFHeaderLineType.valueOf(mapping.get("Type")); } catch (Exception e) { throw new TribbleException(mapping.get("Type") + " is not a valid type in the VCF specification (note that types are case-sensitive)");
type = VCFHeaderLineType.valueOf(mapping.get("Type")); } catch (Exception e) { throw new TribbleException(mapping.get("Type") + " is not a valid type in the VCF specification (note that types are case-sensitive)");
break; default: meta.add(new VCFFormatHeaderLine(formatFields.get(i), 1, VCFHeaderLineType.valueOf(formatFieldsType.get(i)), formatFieldsDescr.get(i))); break;
header.addMetaDataLine(new VCFFormatHeaderLine(id, 1, VCFHeaderLineType.valueOf(line.getType()), ""));
if (Objects.equals(line.getNumber(), "1")) { try { type = VCFHeaderLineType.valueOf(line.getType()); } catch (IllegalArgumentException ignore) { type = VCFHeaderLineType.String;