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 {
if (vcfLine.isFixedCount()) { number = String.valueOf(vcfLine.getCount()); } else if (vcfLine.getCountType().equals(VCFHeaderLineCount.UNBOUNDED)) { number = "."; } else {
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;