---

type: allele_score

table:
  filename: SFARI_SSC_WGS_CSHL-freq.txt.gz
  format: tabix

  chrom:
    name: CHROM
  pos_begin:
    name: POS
  pos_end:
    name: POS
  reference:
    name: REF
  alternative:
    name: ALT

scores:
  - id: parents_called
    name: parents_called
    type: int
    desc: "SFARI SSC WGS CSHL parents called"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 5000
      y_log_scale: True
  - id: allele_count
    name: allele_count
    type: int
    desc: "SFARI SSC WGS CSHL allele count"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0
        max: 10000
      y_log_scale: True
  - id: allele_frequency
    name: allele_frequency
    type: float
    desc: "SFARI SSC WGS CSHL allele frequency in %"
    histogram:
      type: number
      number_of_bins: 101
      view_range:
        min: 0.0
        max: 100.0
      y_log_scale: True
      x_log_scale: True
      x_min_log: 0.01


# histograms:
#   - score: allele_frequency
#     bins: 101
#     min: 0
#     max: 100
#     y_scale: "log"
#     x_scale: "log"
#     x_min_log: 0.01


default_annotation:
  - source: allele_frequency
    name: ssc_freq

meta: 

  summary: |
    Exported from SFARI_SSC_WGS_CSHL using `gpf_validation_data/data_hg38/exports/SFARI_SSC_WGS_CSHL_frequency`.

  description: |
    TODO

    exported from SFARI_SSC_WGS_CSHL using 
    `gpf_validation_data/data_hg38/exports/SFARI_SSC_WGS_CSHL_frequency` scripts

  labels:
    reference_genome: hg38/genomes/GRCh38-hg38