@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; }
switch (line.getKey()) { case "FORMAT": if (count.equals(VCFHeaderLineCount.INTEGER)) { headerLine = new VCFFormatHeaderLine(line.getId(), Integer.parseInt(line.getNumber()), type, line.getDescription()); } else { if (count.equals(VCFHeaderLineCount.INTEGER)) { headerLine = new VCFInfoHeaderLine(line.getId(), Integer.parseInt(line.getNumber()), type, line.getDescription()); } else {
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; }
return line.getType().equals(VCFHeaderLineType.Integer) && line.getCount()==1; else if(id.equals(VCFConstants.GENOTYPE_PL_KEY)) return line.getType().equals(VCFHeaderLineType.Integer) && line.getCountType().equals(VCFHeaderLineCount.G); else if(id.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) return line.getType().equals(VCFHeaderLineType.Integer) && line.getCountType().equals(VCFHeaderLineCount.R); else if(id.equals(VCFConstants.GENOTYPE_FILTER_KEY)) return line.getType().equals(VCFHeaderLineType.String) && line.getCountType().equals(VCFHeaderLineCount.UNBOUNDED); else if(id.equals(VCFConstants.PHASE_QUALITY_KEY)) return line.getType().equals(VCFHeaderLineType.Float) && line.getCount()==1; return line.getType().equals(VCFHeaderLineType.Float) && line.getCount()==1; else if(id.equals(VCFConstants.ALLELE_FREQUENCY_KEY)) return line.getType().equals(VCFHeaderLineType.Float) && line.getCountType().equals(VCFHeaderLineCount.A); else if(id.equals(VCFConstants.ALLELE_COUNT_KEY)) return line.getType().equals(VCFHeaderLineType.Integer) && line.getCountType().equals(VCFHeaderLineCount.A); else if(id.equals(VCFConstants.ALLELE_NUMBER_KEY)) return line.getType().equals(VCFHeaderLineType.Integer) && line.getCount()==1;
@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; }