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VCF fix #249

Merged
merged 18 commits into from
Aug 14, 2020
Merged

VCF fix #249

merged 18 commits into from
Aug 14, 2020

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ch-kr
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@ch-kr ch-kr commented Aug 13, 2020

Fixes for bugs found at runtime

ch-kr and others added 16 commits August 6, 2020 14:59
@ch-kr
Changed adj label in qual hists to raw in make_hist_bin_edges_expr
d75aa6b
@ch-kr
Changed AS_pab_max in INFO_DICT to pab_max
85ea8dd
@ch-kr
Removed AS_pab_max from INFO_DICT and added pab max description as co…
18bc326 
…nstant to add_as_info_dict
@ch-kr
Added description text to apply to all info descriptions in make_info…
05f7aa4 
…_dict
@ch-kr
Updated as info dict to ignore fields that aren't present (rather tha…
5a42332 
…n erroring out)
@ch-kr
Changed make_info_dict to have pop_names arg and removed default from…
98a504b 
… make_combo_header_text
@ch-kr
Changed SORT_ORDER to make sure adj label gets added to end of descri…
a2bfa07 
…ption (gnomad_exomes_AC_asj_adj instead of gnomad_exomes_AC_adj_asj)
@ch-kr
Fixed make_hist_bin_edges_expr to properly pull both raw and adj qual…
0ae87e5 
… hists
@ch-kr
Fixed typo in set_female_metrics_to_na
ba509eb
@jkgoodrich
Fix missing _ in sample_sum_check
3625c8c
@jkgoodrich
Fix for sanity checks subpop and group needed to be swapped
9084931
@jkgoodrich
fix to RF and VQSR field names and info names
8436339
@ch-kr
Renamed culprit in INFO_DICT (VQSR_culprit > culprit)
19d90ca
@ch-kr
Added END to SPARSE_ENTRIES
1e9c31a
@ch-kr
Added missing quotes to Number description for n_alt_alleles
c4fc510
@ch-kr
Updated RF VCF description
b397671
@ch-kr ch-kr requested review from jkgoodrich and gtiao August 13, 2020 20:05
gtiao
gtiao approved these changes Aug 14, 2020
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This looks good to me!

jkgoodrich
jkgoodrich reviewed Aug 14, 2020
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Two really small comments that you can take or leave, but then it is ready

gnomad/utils/vcf.py Show resolved Hide resolved
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jkgoodrich
jkgoodrich approved these changes Aug 14, 2020
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Good to go

@ch-kr ch-kr merged commit 8158797 into master Aug 14, 2020
@ch-kr ch-kr deleted the vcf_fix branch August 14, 2020 14:49
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@jkgoodrich jkgoodrich jkgoodrich approved these changes

@gtiao gtiao gtiao approved these changes

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3 participants
@ch-kr @gtiao @jkgoodrich