export default {
  // INFO fields
  InfoFields: {
    // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf
    AA: { Number: 1, Type: 'String', Description: 'Ancestral allele' },
    AC: {
      Number: 'A',
      Type: 'Integer',
      Description:
        'Allele count in genotypes, for each ALT allele, in the same order as listed',
    },
    AD: {
      Number: 'R',
      Type: 'Integer',
      Description: 'Total read depth for each allele',
    },
    ADF: {
      Number: 'R',
      Type: 'Integer',
      Description: 'Read depth for each allele on the forward strand',
    },
    ADR: {
      Number: 'R',
      Type: 'Integer',
      Description: 'Read depth for each allele on the reverse strand',
    },
    AF: {
      Number: 'A',
      Type: 'Float',
      Description:
        'Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes)',
    },
    AN: {
      Number: 1,
      Type: 'Integer',
      Description: 'Total number of alleles in called genotypes',
    },
    BQ: {
      Number: 1,
      Type: 'Float',
      Description: 'RMS base quality',
    },
    CIGAR: {
      Number: 1,
      Type: 'Float',
      Description:
        'Cigar string describing how to align an alternate allele to the reference allele',
    },
    DB: {
      Number: 0,
      Type: 'Flag',
      Description: 'dbSNP membership',
    },
    DP: {
      Number: 1,
      Type: 'Integer',
      Description: 'combined depth across samples',
    },
    END: {
      Number: 1,
      Type: 'Integer',
      Description: 'End position (for use with symbolic alleles)',
    },
    H2: {
      Number: 0,
      Type: 'Flag',
      Description: 'HapMap2 membership',
    },
    H3: {
      Number: 0,
      Type: 'Flag',
      Description: 'HapMap3 membership',
    },
    MQ: {
      Number: 1,
      Type: null,
      Description: 'RMS mapping quality',
    },
    MQ0: {
      Number: 1,
      Type: 'Integer',
      Description: 'Number of MAPQ == 0 reads',
    },
    NS: {
      Number: 1,
      Type: 'Integer',
      Description: 'Number of samples with data',
    },
    SB: {
      Number: 4,
      Type: 'Integer',
      Description: 'Strand bias',
    },
    SOMATIC: {
      Number: 0,
      Type: 'Flag',
      Description: 'Somatic mutation (for cancer genomics)',
    },
    VALIDATED: {
      Number: 0,
      Type: 'Flag',
      Description: 'Validated by follow-up experiment',
    },
    '1000G': {
      Number: 0,
      Type: 'Flag',
      Description: '1000 Genomes membership',
    },
    // specifically for structural variants
    IMPRECISE: {
      Number: 0,
      Type: 'Flag',
      Description: 'Imprecise structural variation',
    },
    NOVEL: {
      Number: 0,
      Type: 'Flag',
      Description: 'Indicates a novel structural variation',
    },
    // For precise variants, END is POS + length of REF allele - 1,
    // and the for imprecise variants the corresponding best estimate.
    SVTYPE: {
      Number: 1,
      Type: 'String',
      Description: 'Type of structural variant',
    },
    // Value should be one of DEL, INS, DUP, INV, CNV, BND. This key can
    // be derived from the REF/ALT fields but is useful for filtering.
    SVLEN: {
      Number: null,
      Type: 'Integer',
      Description: 'Difference in length between REF and ALT alleles',
    },
    // One value for each ALT allele. Longer ALT alleles (e.g. insertions)
    // have positive values, shorter ALT alleles (e.g. deletions)
    // have negative values.
    CIPOS: {
      Number: 2,
      Type: 'Integer',
      Description: 'Confidence interval around POS for imprecise variants',
    },
    CIEND: {
      Number: 2,
      Type: 'Integer',
      Description: 'Confidence interval around END for imprecise variants',
    },
    HOMLEN: {
      Type: 'Integer',
      Description:
        'Length of base pair identical micro-homology at event breakpoints',
    },
    HOMSEQ: {
      Type: 'String',
      Description:
        'Sequence of base pair identical micro-homology at event breakpoints',
    },
    BKPTID: {
      Type: 'String',
      Description: 'ID of the assembled alternate allele in the assembly file',
    },
    // For precise variants, the consensus sequence the alternate allele assembly
    // is derivable from the REF and ALT fields. However, the alternate allele
    // assembly file may contain additional information about the characteristics
    // of the alt allele contigs.
    MEINFO: {
      Number: 4,
      Type: 'String',
      Description: 'Mobile element info of the form NAME,START,END,POLARITY',
    },
    METRANS: {
      Number: 4,
      Type: 'String',
      Description:
        'Mobile element transduction info of the form CHR,START,END,POLARITY',
    },
    DGVID: {
      Number: 1,
      Type: 'String',
      Description: 'ID of this element in Database of Genomic Variation',
    },
    DBVARID: {
      Number: 1,
      Type: 'String',
      Description: 'ID of this element in DBVAR',
    },
    DBRIPID: {
      Number: 1,
      Type: 'String',
      Description: 'ID of this element in DBRIP',
    },
    MATEID: {
      Number: null,
      Type: 'String',
      Description: 'ID of mate breakends',
    },
    PARID: {
      Number: 1,
      Type: 'String',
      Description: 'ID of partner breakend',
    },
    EVENT: {
      Number: 1,
      Type: 'String',
      Description: 'ID of event associated to breakend',
    },
    CILEN: {
      Number: 2,
      Type: 'Integer',
      Description:
        'Confidence interval around the inserted material between breakend',
    },
    DPADJ: { Type: 'Integer', Description: 'Read Depth of adjacency' },
    CN: {
      Number: 1,
      Type: 'Integer',
      Description: 'Copy number of segment containing breakend',
    },
    CNADJ: {
      Number: null,
      Type: 'Integer',
      Description: 'Copy number of adjacency',
    },
    CICN: {
      Number: 2,
      Type: 'Integer',
      Description: 'Confidence interval around copy number for the segment',
    },
    CICNADJ: {
      Number: null,
      Type: 'Integer',
      Description: 'Confidence interval around copy number for the adjacency',
    },
  },

  // FORMAT fields
  GenotypeFields: {
    // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf
    AD: {
      Number: 'R',
      Type: 'Integer',
      Description: 'Read depth for each allele',
    },
    ADF: {
      Number: 'R',
      Type: 'Integer',
      Description: 'Read depth for each allele on the forward strand',
    },
    ADR: {
      Number: 'R',
      Type: 'Integer',
      Description: 'Read depth for each allele on the reverse strand',
    },
    DP: {
      Number: 1,
      Type: 'Integer',
      Description: 'Read depth',
    },
    EC: {
      Number: 'A',
      Type: 'Integer',
      Description: 'Expected alternate allele counts',
    },
    FT: {
      Number: 1,
      Type: 'String',
      Description: 'Filter indicating if this genotype was "called"',
    },
    GL: {
      Number: 'G',
      Type: 'Float',
      Description: 'Genotype likelihoods',
    },
    GP: {
      Number: 'G',
      Type: 'Float',
      Description: 'Genotype posterior probabilities',
    },
    GQ: {
      Number: 1,
      Type: 'Integer',
      Description: 'Conditional genotype quality',
    },
    GT: {
      Number: 1,
      Type: 'String',
      Description: 'Genotype',
    },
    HQ: {
      Number: 2,
      Type: 'Integer',
      Description: 'Haplotype quality',
    },
    MQ: {
      Number: 1,
      Type: 'Integer',
      Description: 'RMS mapping quality',
    },
    PL: {
      Number: 'G',
      Type: 'Integer',
      Description:
        'Phred-scaled genotype likelihoods rounded to the closest integer',
    },
    PQ: {
      Number: 1,
      Type: 'Integer',
      Description: 'Phasing quality',
    },
    PS: {
      Number: 1,
      Type: 'Integer',
      Description: 'Phase set',
    },
  },

  // ALT fields
  AltTypes: {
    DEL: {
      Description: 'Deletion relative to the reference',
    },
    INS: {
      Description: 'Insertion of novel sequence relative to the reference',
    },
    DUP: {
      Description: 'Region of elevated copy number relative to the reference',
    },
    INV: {
      Description: 'Inversion of reference sequence',
    },
    CNV: {
      Description:
        'Copy number variable region (may be both deletion and duplication)',
    },
    'DUP:TANDEM': {
      Description: 'Tandem duplication',
    },
    'DEL:ME': {
      Description: 'Deletion of mobile element relative to the reference',
    },
    'INS:ME': {
      Description: 'Insertion of a mobile element relative to the reference',
    },
    NON_REF: {
      Description:
        'Represents any possible alternative allele at this location',
    },
    '*': {
      Description:
        'Represents any possible alternative allele at this location',
    },
  },

  // FILTER fields
  FilterTypes: {
    PASS: {
      Description: 'Passed all filters',
    },
  },
}