//
// VCF header line constants
//
static {
// FORMAT lines
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "Genotype Quality"));
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.DEPTH_KEY,
1,
VCFHeaderLineType.Integer,
"Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.GENOTYPE_PL_KEY,
VCFHeaderLineCount.G,
VCFHeaderLineType.Integer,
"Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.GENOTYPE_ALLELE_DEPTHS,
VCFHeaderLineCount.R,
VCFHeaderLineType.Integer,
"Allelic depths for the ref and alt alleles in the order listed"));
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.GENOTYPE_FILTER_KEY,
VCFHeaderLineCount.UNBOUNDED,
VCFHeaderLineType.String,
"Genotype-level filter"));
registerStandard(
new VCFFormatHeaderLine(
VCFConstants.PHASE_QUALITY_KEY,
1,
VCFHeaderLineType.Float,
"Read-backed phasing quality"));
// INFO lines
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.DBSNP_KEY, 0, VCFHeaderLineType.Flag, "dbSNP Membership"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.DEPTH_KEY,
1,
VCFHeaderLineType.Integer,
"Approximate read depth; some reads may have been filtered"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.STRAND_BIAS_KEY, 1, VCFHeaderLineType.Float, "Strand Bias"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.ALLELE_FREQUENCY_KEY,
VCFHeaderLineCount.A,
VCFHeaderLineType.Float,
"Allele Frequency, for each ALT allele, in the same order as listed"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.ALLELE_COUNT_KEY,
VCFHeaderLineCount.A,
VCFHeaderLineType.Integer,
"Allele count in genotypes, for each ALT allele, in the same order as listed"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.ALLELE_NUMBER_KEY,
1,
VCFHeaderLineType.Integer,
"Total number of alleles in called genotypes"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.MAPPING_QUALITY_ZERO_KEY,
1,
VCFHeaderLineType.Integer,
"Total Mapping Quality Zero Reads"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.RMS_MAPPING_QUALITY_KEY,
1,
VCFHeaderLineType.Float,
"RMS Mapping Quality"));
registerStandard(
new VCFInfoHeaderLine(
VCFConstants.SOMATIC_KEY, 0, VCFHeaderLineType.Flag, "Somatic event"));
}
