public static VCFHeaderLineType getVCFHeaderLineType(VariantFileHeaderComplexLine line) { if (StringUtils.isEmpty(line.getType())) { return null; } else { return VCFHeaderLineType.valueOf(line.getType()); } }
/**Return Object unk as a string quoted or not quoted depending on its type * and suitable for a javascript script. * */ private String formatObjectForJS(String key, Object unk, VCFHeaderLineType type) { if(unk == null){ return "null"; // Can this actually happen? } if(type.equals(VCFHeaderLineType.Flag) || type.equals(VCFHeaderLineType.Integer) || type.equals(VCFHeaderLineType.Float)){ return unk.toString(); } else { return '"' + unk.toString() + '"'; } }
@Override public int hashCode() { int result = super.hashCode(); result = 31 * result + name.hashCode(); result = 31 * result + count; result = 31 * result + (countType != null ? countType.hashCode() : 0); // only nullable field according to validate() result = 31 * result + description.hashCode(); result = 31 * result + type.hashCode(); result = 31 * result + lineType.hashCode(); result = 31 * result + (source != null ? source.hashCode() : 0); result = 31 * result + (version != null ? version.hashCode() : 0); return result; }
"Sample genotype filter. Similar in concept to the FILTER field.", ".", VCFHeaderLineType.String.toString(), null); studyConfiguration.getVariantHeader().getComplexLines().add(line); } else { if (Objects.equals(line.getNumber(), "1")) { try { type = VCFHeaderLineType.valueOf(line.getType()); } catch (IllegalArgumentException ignore) { type = VCFHeaderLineType.String; extraFieldsType.add(type.toString()); logger.debug(extraFormatField + " : " + type);
VCFFormatHeaderLine formatHeaderLine = (VCFFormatHeaderLine) headerLine; boolean isGT = formatHeaderLine.getID().equals(VCFConstants.GENOTYPE_KEY); String genomicsDBType = isGT ? "int" : formatHeaderLine.getType().toString(); String genomicsDBLength = isGT ? "P" : (formatHeaderLine.getType() == VCFHeaderLineType.String) ? "VAR" : getLength(formatHeaderLine); VCFInfoHeaderLine infoHeaderLine = (VCFInfoHeaderLine) headerLine; if (infoHeaderLine.getType().equals(VCFHeaderLineType.Flag)) { System.err.println("WARNING: Flag type fields are not handled by GenomicsDB currently - skipping field " +infoHeaderLine.getID()); .setType(infoHeaderLine.getType().toString()) .setLength(infoHeaderLine.getType() == VCFHeaderLineType.String ? "var" : getLength(infoHeaderLine));
.setId(vcfLine.getID()) .setDescription(vcfLine.getDescription()) .setType(vcfLine.getType().toString()) .setNumber(number).build());
private VariantSetMetadata convert(VCFCompoundHeaderLine hl) { VariantSetMetadata vsm = convertHeaderLine((VCFHeaderLine) hl); vsm.setId(hl.getID()); if (hl.isFixedCount()) { vsm.setNumber(Integer.toString(hl.getCount())); } else { vsm.setNumber(hl.getCountType().name()); } vsm.setType(hl.getType().name()); vsm.setDescription(hl.getDescription()); // Empty for the moment Map<String, List<String>> infoMap = Collections.emptyMap(); vsm.setInfo(infoMap); return vsm; }
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; }
public String rearrange(String key, String data, @Nullable Integer ploidy) { if (StringUtils.isEmpty(data) || data.equals(".")) { // Do not rearrange missing values return data; } Pair<VCFHeaderLineType, VCFHeaderLineCount> pair = configuration.otherFieldsMap.getOrDefault(key, Pair.of(VCFHeaderLineType.String, VCFHeaderLineCount.UNBOUNDED)); VCFHeaderLineType type = pair.getLeft(); String missingValue = type.equals(VCFHeaderLineType.Float) || type.equals(VCFHeaderLineType.Integer) ? "0" : "."; try { switch (pair.getRight()) { case A: data = rearrangeNumberA(data, missingValue); break; case R: data = rearrangeNumberR(data, missingValue); break; case G: data = rearrangeNumberG(data, missingValue, ploidy); break; case INTEGER: case UNBOUNDED: default: // Do not rearrange other fields } } catch (IllegalArgumentException e) { throw new IllegalArgumentException("Error rearranging key " + key + " = " + data, e); } return data; }
@Override public int hashCode() { int result = super.hashCode(); result = 31 * result + name.hashCode(); result = 31 * result + count; result = 31 * result + (countType != null ? countType.hashCode() : 0); // only nullable field according to validate() result = 31 * result + description.hashCode(); result = 31 * result + type.hashCode(); result = 31 * result + lineType.hashCode(); return result; }
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; }
refAnnotated, ImmutableList.of(fieldName), ImmutableMap.of(fieldName, new GenericTSVValueColumnDescription(colValue, VCFHeaderLineType.valueOf(fieldType), fieldName, fieldDescription, GenericTSVAccumulationStrategy.valueOf(accStrategy))));
fmtValue= this.formatObjectForJS(key, unkValue, vcfHeader.getInfoHeaderLine(key).getType()); } catch(NullPointerException e){ if(headerLine.getType().equals(VCFHeaderLineType.Flag)){
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)");
if (compLine.getType().equals(compOther.getType())) {
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)");
if ( compLine.getType().equals(compOther.getType()) ) {
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)");
if (compLine.getType().equals(compOther.getType())) {