Code

VCF fix#249

Code

Merged

ch-kr merged 18 commits intomasterbroadinstitute/gnomad_methods:masterfrom vcf_fixbroadinstitute/gnomad_methods:vcf_fixCopy head branch name to clipboardAug 14, 2020

+51-37

Commits

Commits on Aug 6, 2020

• Changed adj label in qual hists to raw in make_hist_bin_edges_expr

  ch-kr

  committed
  d75aa6b

• Changed AS_pab_max in INFO_DICT to pab_max

  ch-kr

  committed
  85ea8dd

• Removed AS_pab_max from INFO_DICT and added pab max description as constant to add_as_info_dict

  ch-kr

  committed
  18bc326

Commits on Aug 7, 2020

• Added description text to apply to all info descriptions in make_info_dict

  ch-kr

  committed
  05f7aa4

• Updated as info dict to ignore fields that aren't present (rather than erroring out)

  ch-kr

  committed
  5a42332

• Changed make_info_dict to have pop_names arg and removed default from make_combo_header_text

  ch-kr

  committed
  98a504b

• Changed SORT_ORDER to make sure adj label gets added to end of description (gnomad_exomes_AC_asj_adj instead of gnomad_exomes_AC_adj_asj)

  ch-kr

  committed
  a2bfa07

• Fixed make_hist_bin_edges_expr to properly pull both raw and adj qual hists

  ch-kr

  committed
  0ae87e5

• Fixed typo in set_female_metrics_to_na

  ch-kr

  committed
  ba509eb

• Fix missing _ in sample_sum_check

  jkgoodrich

  committed
  3625c8c

Commits on Aug 8, 2020

• Fix for sanity checks subpop and group needed to be swapped

  jkgoodrich

  committed
  9084931

Commits on Aug 10, 2020

• fix to RF and VQSR field names and info names

  jkgoodrich

  committed
  8436339

• Renamed culprit in INFO_DICT (VQSR_culprit > culprit)

  ch-kr

  committed
  19d90ca

• Added END to SPARSE_ENTRIES

  ch-kr

  committed
  1e9c31a

• Added missing quotes to Number description for n_alt_alleles

  ch-kr

  committed
  c4fc510

Commits on Aug 13, 2020

• Updated RF VCF description

  ch-kr

  committed
  b397671

• Updated changelog with vcf fixes

  ch-kr

  committed
  5494d87

Commits on Aug 14, 2020

• Updated RF description

  ch-kr

  committed
  9073d7a