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20a4e7e
Add `annotate_allele_info` function to annotations.py
jkgoodrich May 4, 2023
6d30766
Rearrange docstring based on annotation order
jkgoodrich May 4, 2023
80ec015
Update annotations.py
matren395 May 8, 2023
f9d2a7b
Update annotations.py
matren395 May 9, 2023
fa6bfd4
Add ability to use allele specific annotations in the gvcf_info field
jkgoodrich May 10, 2023
9985815
Apply suggestions from code review
matren395 May 11, 2023
d18e1c6
Update annotations.py
matren395 May 11, 2023
c0ac756
Update annotations.py
matren395 May 11, 2023
b22197d
Update annotations.py
matren395 May 12, 2023
26c99f8
Update annotations.py
matren395 May 15, 2023
e5dbbb1
Apply suggestions from code review
matren395 May 17, 2023
e4956f1
Update annotations.py
matren395 May 17, 2023
377bd69
Update annotations.py
matren395 May 17, 2023
36b64b0
Apply suggestions from code review
matren395 May 19, 2023
d811c4b
Update annotations.py
matren395 May 19, 2023
a1e8fc9
Update annotations.py
matren395 May 21, 2023
8bd283f
Apply suggestions from code review
matren395 May 22, 2023
01c5e30
update hl.cond to hl.if_else
KoalaQin May 22, 2023
0868da8
change VEP CSQ FIELDs to VEP 105
KoalaQin May 22, 2023
2ec4d3c
remove VEP CSQ fields in the colocated_variants subfield
KoalaQin May 22, 2023
8987051
Update annotations.py
matren395 May 22, 2023
cf2095f
Update annotations.py
matren395 May 23, 2023
737eedc
Update annotations.py
matren395 May 23, 2023
4dd1b60
Update annotations.py
matren395 May 23, 2023
ddca8b4
Apply suggestions from code review
matren395 May 24, 2023
f64795c
Update annotations.py
matren395 May 24, 2023
c97fe5a
Move gnomad_gks()
matren395 May 24, 2023
e04691e
Update gnomad.py
matren395 May 24, 2023
08682a3
Add GRCh37 SeqIDs and change Coverage HT logic
matren395 May 24, 2023
03044bf
Update annotations.py
matren395 May 24, 2023
c6ec474
Formatting changes for gnomad.py
matren395 May 25, 2023
925b4ac
Update annotations.py
matren395 May 25, 2023
1a752c0
Apply suggestions from code review
matren395 May 25, 2023
88f7309
Update gnomad.py
matren395 May 25, 2023
3e5da3e
fomratting - docstrings and adding ga4gh.vrs to requirements
matren395 May 25, 2023
becf9ce
Update annotations.py
matren395 May 25, 2023
c453934
Update annotations.py
matren395 May 25, 2023
22ab092
Add variant to "id"s, and some changes to logic of reading in coverag…
matren395 May 25, 2023
4a085e7
Update annotations.py
matren395 May 26, 2023
2f275ce
Apply suggestions from code review
matren395 May 26, 2023
4f6de00
Warnings and Logic
matren395 May 26, 2023
6e11d1b
Change Non-v3 Not Implemented Error message
matren395 May 26, 2023
6ee24bc
remove 4 missing fields from VEP105
KoalaQin Jun 7, 2023
14819af
Merge N freq arrays by sum only
mike-w-wilson Jun 7, 2023
1f58568
Add subtraction
mike-w-wilson Jun 8, 2023
87fd2fd
Update diff dictionary and add comments
mike-w-wilson Jun 8, 2023
634ab95
Switch to Julia's merge
mike-w-wilson Jun 9, 2023
3499e40
Add diff back with options for negative values
mike-w-wilson Jun 14, 2023
4d374d2
Add description of function
mike-w-wilson Jun 14, 2023
3aa7f68
Drop TODOs
mike-w-wilson Jun 14, 2023
55340de
Update gnomad/utils/annotations.py
mike-w-wilson Jun 14, 2023
2d40b72
Update gnomad/utils/annotations.py
mike-w-wilson Jun 14, 2023
ac50e04
Move to same module as original function
mike-w-wilson Jun 14, 2023
8c29fb8
Update imports
mike-w-wilson Jun 14, 2023
ce76d83
Remove unnecessary imports
mike-w-wilson Jun 14, 2023
93be0d3
Apply suggestions from code review
mike-w-wilson Jun 14, 2023
0d4a67a
update merge docs
mike-w-wilson Jun 14, 2023
19f3c26
update merge docs
mike-w-wilson Jun 14, 2023
50c2b22
Black is misformating these, hail errors without them
mike-w-wilson Jun 14, 2023
6b75bfa
Add Siwei's methylation bed file to grch38 resources
jkgoodrich Jun 14, 2023
914b313
Add key_by locus
jkgoodrich Jun 14, 2023
c4d65b8
Apply suggestions from code review
mike-w-wilson Jun 21, 2023
e6ad87f
Add AF to correction for when AC < 0
mike-w-wilson Jun 21, 2023
95bf58c
Set default to error
mike-w-wilson Jun 21, 2023
980b1e8
Remove optional sort_order, add warning and docs
mike-w-wilson Jun 21, 2023
f006281
add optional ab_expr to qual_hists
mike-w-wilson Jun 22, 2023
bc75879
Update gnomad/utils/annotations.py
mike-w-wilson Jun 22, 2023
7a7ea7d
Merge branch 'main' of https://github.com/broadinstitute/gnomad_metho…
jkgoodrich Jun 22, 2023
589a2fc
Apply suggestions from code review
mike-w-wilson Jun 23, 2023
65de216
Fix return doc and prevent formatting that breaks hail
mike-w-wilson Jun 23, 2023
8fd0ef9
Make sort_order optional
mike-w-wilson Jun 23, 2023
00418c6
Handle diff error when sort_order None is passed
mike-w-wilson Jun 23, 2023
1013b60
Logger for ab hist expr and fix label
mike-w-wilson Jun 23, 2023
320d4e2
Merge pull request #555 from broadinstitute/mw/add_ab_expr_to_qual_hists
mike-w-wilson Jun 23, 2023
f9c2f0f
Merge pull request #551 from broadinstitute/mw/merge_freq_arrays
mike-w-wilson Jun 23, 2023
5826d02
Address review comments
jkgoodrich Jun 26, 2023
fb5cbcc
Merge branch 'main' of https://github.com/broadinstitute/gnomad_metho…
jkgoodrich Jun 26, 2023
3befde4
Merge pull request #552 from broadinstitute/jg/add_grch38_methylation…
jkgoodrich Jun 26, 2023
d467939
Merge remote-tracking branch 'origin/main' into qh/v4_vep_vcf
KoalaQin Jun 27, 2023
8bc2e39
add vep versions to gnomad.py
KoalaQin Jun 27, 2023
1043918
make csq fields to current VEP version
KoalaQin Jun 27, 2023
fd7e183
make VEP_VERSIONS inside vep.py
KoalaQin Jun 27, 2023
97b2b12
keep gnomad.py unchanged
KoalaQin Jun 27, 2023
7060e65
keep gnomad.py unchanged
KoalaQin Jun 27, 2023
6a3ab9a
allow for boolean expression in `comparison_sample_expr`
jkgoodrich Jun 27, 2023
8aec570
change docstring of csq_fields
KoalaQin Jun 28, 2023
33aa1b9
Merge pull request #546 from broadinstitute/qh/v4_vep_vcf
KoalaQin Jun 28, 2023
ced5cd7
Merge branch 'main' of https://github.com/broadinstitute/gnomad_metho…
jkgoodrich Jun 28, 2023
5121ca5
Add to docstring for `comparison_sample_expr`
jkgoodrich Jun 29, 2023
5b62076
Updates to `assign_population_pcs` to use onnx models
jkgoodrich Jun 30, 2023
2d20af2
Merge pull request #557 from broadinstitute/jg/outlier_filtering_incl…
jkgoodrich Jul 1, 2023
c775ffd
Fix model check in `convert_sklearn_rf_to_onnx`
jkgoodrich Jul 1, 2023
8b9f87e
remove unneeded fstring
jkgoodrich Jul 1, 2023
d0cce17
Fixes to allele specific annotation aggregation after testing
jkgoodrich Jul 1, 2023
64b0117
Remove AS_RAW_MQ from AS_INFO_ARRAY_SUM_AGG_FIELDS
jkgoodrich Jul 7, 2023
c8146ba
Merge pull request #558 from broadinstitute/jg/modify_pop_assign_for_…
jkgoodrich Jul 10, 2023
abb8187
Add count array merge
mike-w-wilson Jul 18, 2023
62e7c63
Add count error msg
mike-w-wilson Jul 18, 2023
2eb04cf
Add `sample_list_stratification` option to `create_fake_pedigree` fun…
jkgoodrich Jul 18, 2023
2115597
Apply suggestions from code review
jkgoodrich Jul 18, 2023
4935ff2
turn info agg globals into a dict
jkgoodrich Jul 18, 2023
517f2c5
Merge branch 'jg/change_compute_info_to_use_AS_ann' of https://github…
jkgoodrich Jul 18, 2023
61a85c7
Address review comments
jkgoodrich Jul 19, 2023
7e0d001
Merge pull request #564 from broadinstitute/jg/add_strat_to_fake_trios
jkgoodrich Jul 19, 2023
c0c17e7
Fix missed variable name change and bug
mike-w-wilson Jul 20, 2023
cd7a81a
Modify `annotate_adj` to use LGT and LAD if present
jkgoodrich Jul 20, 2023
1fc3df9
Modify `annotate_adj` to use LGT and LAD if present
jkgoodrich Jul 20, 2023
24c069e
Merge pull request #560 from broadinstitute/jg/change_compute_info_to…
jkgoodrich Jul 27, 2023
511b8d7
Merge pull request #567 from broadinstitute/jg/modify_annotate_adj_fo…
jkgoodrich Jul 27, 2023
3f49f84
run `pip-compile --upgrade requirements-dev.in` and `pip-compile --up…
jkgoodrich Aug 1, 2023
1eefe6a
Merge pull request #569 from broadinstitute/jg/pip_compile_update
jkgoodrich Aug 1, 2023
8273a8b
Function to annotate downsamplings onto HT/MT
mike-w-wilson Aug 2, 2023
10f4dfa
Merge pull request #570 from broadinstitute/mw/ann_downsamplings
mike-w-wilson Aug 2, 2023
faa26c3
Split VDS by strata
mike-w-wilson Aug 2, 2023
9f4f0b7
Add compute freq by strata for use in annotate_freq
mike-w-wilson Aug 2, 2023
2acb730
Update annotate_freq to use compute_freq_by_strata
mike-w-wilson Aug 2, 2023
0106f08
Explain raw additions
mike-w-wilson Aug 2, 2023
2521ec4
Add option to split adj histograms out from raw before return
mike-w-wilson Aug 3, 2023
4263f07
Add docstring to split adj histograms out from raw before return
mike-w-wilson Aug 3, 2023
8fe0457
Docs for compute_freq_by_strata
mike-w-wilson Aug 3, 2023
dd7b65e
A few more docs for new functions
mike-w-wilson Aug 3, 2023
1911962
Add function to merge histograms with the same bin_edges
mike-w-wilson Aug 3, 2023
389622f
Apply suggestions from code review
mike-w-wilson Aug 3, 2023
f02cc53
Merge pull request #572 from broadinstitute/mw/merge_histogram
mike-w-wilson Aug 3, 2023
be87522
Speed up GKS annotations and add interval based annotation (#559)
theferrit32 Aug 3, 2023
71131a0
Update docs for annotate_freq
mike-w-wilson Aug 4, 2023
44d37d7
Add errors around ds expectations in compute_freq_by_strata
mike-w-wilson Aug 4, 2023
1ce6f65
Add errors around ds expectations in compute_freq_by_strata
mike-w-wilson Aug 4, 2023
974c846
Comments on compute_freq_by_strata
mike-w-wilson Aug 4, 2023
ccd8d5c
Clarify returns and generalize inline comments
mike-w-wilson Aug 4, 2023
5d837ef
Merge branch 'main' into mw/merge_ab_hets
jkgoodrich Aug 4, 2023
6d8dd71
Missed data types and docs
mike-w-wilson Aug 4, 2023
057e2e7
Merge pull request #565 from broadinstitute/mw/merge_ab_hets
mike-w-wilson Aug 4, 2023
249c3de
Apply suggestions from code review
mike-w-wilson Aug 4, 2023
d5e495f
Merge pull request #571 from broadinstitute/mw/compute_freq_by_strata
mike-w-wilson Aug 4, 2023
363b9d3
A few small type changes
jkgoodrich Aug 4, 2023
0cfee66
Merge pull request #573 from broadinstitute/jg/tiny_type_change
jkgoodrich Aug 4, 2023
db12d9b
Fix callstats order in `merge_freq_arrays`
jkgoodrich Aug 9, 2023
1807bda
Merge pull request #574 from broadinstitute/jg/fix_array_freq_struct_…
jkgoodrich Aug 10, 2023
9244cb5
Replace deprecated Hail hl.cond() function with its replacement
jmarshall May 1, 2023
40d055a
Modifications to frequency annotation to improve memory use
jkgoodrich Aug 14, 2023
20a3831
Apply suggestions from code review
jkgoodrich Aug 16, 2023
2273906
Address review comments
jkgoodrich Aug 16, 2023
c23119b
Update gnomad/utils/annotations.py
mike-w-wilson Aug 16, 2023
a089bbc
Merge pull request #577 from broadinstitute/jg/frequency_changes_impr…
mike-w-wilson Aug 16, 2023
f7ce832
Update python 3.8 -> 3.11
jkgoodrich Aug 17, 2023
1dda889
Update doc requirements
jkgoodrich Aug 17, 2023
1bb92bb
Update black
jkgoodrich Aug 17, 2023
8b9121b
Update black target versions
jkgoodrich Aug 17, 2023
b25685b
update workflow versions
jkgoodrich Aug 17, 2023
6183ad9
Merge pull request #576 from populationgenomics/avoid-deprecated
jkgoodrich Aug 17, 2023
1579002
Merge pull request #578 from broadinstitute/jg/update_python_version
jkgoodrich Aug 17, 2023
581cd7a
Run count merge through dict of lists rather than single list
mike-w-wilson Aug 17, 2023
12a11ae
Merge pull request #579 from broadinstitute/mw/merge_fmeta_s_counts
mike-w-wilson Aug 17, 2023
c946a0b
function to update sample annotations
KoalaQin Aug 18, 2023
be43606
change return type of add_filters_expr
KoalaQin Aug 18, 2023
d622059
merge from main
KoalaQin Aug 18, 2023
edad95d
re-add function
KoalaQin Aug 18, 2023
a4dc91c
test pre-commit
KoalaQin Aug 18, 2023
af73f09
reverse changing type to pass checks
KoalaQin Aug 18, 2023
6dcc781
move function to release.py
KoalaQin Aug 18, 2023
89de5e2
change return type in add_filters_expr
KoalaQin Aug 18, 2023
3a448cd
add blank line
KoalaQin Aug 18, 2023
541ad88
address review comments
KoalaQin Aug 21, 2023
28fc712
address review comments
KoalaQin Aug 21, 2023
7d90d58
change type
KoalaQin Aug 21, 2023
2bc0a22
change type 2
KoalaQin Aug 21, 2023
aaef59b
reserve to SetExpression for add_filters_expr
KoalaQin Aug 21, 2023
0b355d1
Merge pull request #580 from broadinstitute/qh/updata_annotations
KoalaQin Aug 21, 2023
d1ce1d4
Change split_vds return to dict
mike-w-wilson Aug 22, 2023
399826e
fix circular import of annotate_adj
jkgoodrich Aug 22, 2023
e2142ee
Merge pull request #581 from broadinstitute/jg/fix_circular
jkgoodrich Aug 22, 2023
e409d67
Fix bug in annotate_freq downsampling_expr
mike-w-wilson Aug 23, 2023
6f2d8a0
function to remove items from freq and freq_meta
KoalaQin Aug 24, 2023
30c2ef3
Merge remote-tracking branch 'origin/main' into qh/remove_from_freq
KoalaQin Aug 24, 2023
53e75f1
make it general to list of keys and dict of keys-values
KoalaQin Aug 25, 2023
89c980f
Update docs for split
mike-w-wilson Aug 25, 2023
e838a7a
Merge pull request #583 from broadinstitute/mw/split_vds_change_to_dict
mike-w-wilson Aug 25, 2023
ec030eb
address comment review
KoalaQin Aug 25, 2023
3a52ddc
address comment review
KoalaQin Aug 25, 2023
f1d87a3
add docstring to Julia's versatile version
KoalaQin Aug 25, 2023
a12975d
add docstring to Julia's versatile version
KoalaQin Aug 25, 2023
688eaf1
merge from origin/main
KoalaQin Aug 25, 2023
fe7a612
import Any from typing
KoalaQin Aug 25, 2023
756beb8
Make naive_coalesce optional in `default_compute_info`
jkgoodrich Aug 28, 2023
b2f072f
Update gnomad/utils/sparse_mt.py
jkgoodrich Aug 28, 2023
35e581e
Merge pull request #584 from broadinstitute/jg/compute_info_make_naiv…
jkgoodrich Aug 28, 2023
bc668a4
address review comments round 2
KoalaQin Aug 28, 2023
1e863e1
change fstring
KoalaQin Aug 28, 2023
a4032b7
fix unexpected indentation
KoalaQin Aug 28, 2023
4383dc7
fix unexpected indentation again
KoalaQin Aug 28, 2023
b1d749f
fix unexpected indentation again again
KoalaQin Aug 28, 2023
9888ce5
commit omitted suggestions
KoalaQin Aug 28, 2023
7095e94
Merge pull request #582 from broadinstitute/qh/remove_from_freq
KoalaQin Aug 28, 2023
5e290b2
Add optional freq_meta_sample_count to filtering
mike-w-wilson Aug 29, 2023
4b20c83
Change order of filtering so can use meta for freq sample counts
mike-w-wilson Aug 29, 2023
95dccd5
Change variable name to be less specific
mike-w-wilson Aug 29, 2023
b4997ae
Switch to dict of expressions, allows multiple arrays to be filtered
mike-w-wilson Aug 30, 2023
cab3034
Flip to dict comprehension
mike-w-wilson Aug 30, 2023
2aedfe5
Fix the case where there are more than 2 freqs/fmetas and fmeta doesn…
jkgoodrich Aug 31, 2023
0db45d9
Apply suggestions from code review
mike-w-wilson Aug 31, 2023
3753558
Update gnomad/utils/filtering.py
mike-w-wilson Aug 31, 2023
e6f042a
Merge pull request #587 from broadinstitute/jg/fix_merge_freqs_with_m…
jkgoodrich Aug 31, 2023
0ce44f1
Fix for error Error summary: AssertionError: assertion failed: Key ty…
jkgoodrich Sep 5, 2023
01713a7
fix negative values issue with 'diff'
KoalaQin Sep 6, 2023
0a7aad4
Merge pull request #590 from broadinstitute/qh/merge_freq
KoalaQin Sep 6, 2023
82cc9b3
fix ValueError for count_arrays in merge_freq_arrays function
KoalaQin Sep 6, 2023
1926316
add more info for raise ValueError in merge_freq_arrays
KoalaQin Sep 6, 2023
0ca8b3b
Merge pull request #591 from broadinstitute/qh/merge_freq
KoalaQin Sep 6, 2023
08ce557
Merge pull request #589 from broadinstitute/jg/annotate_downsamplings…
jkgoodrich Sep 6, 2023
24188af
Add flexiility around passed indexed expression type
mike-w-wilson Aug 31, 2023
e48c7b5
Update gnomad/utils/filtering.py
mike-w-wilson Sep 6, 2023
71d25bb
Black on github suggestion
mike-w-wilson Sep 6, 2023
8855a36
Merge pull request #585 from broadinstitute/mw/filter_to_freq_meta_sa…
mike-w-wilson Sep 6, 2023
97f6ab5
Merge branch 'variant_report_code' of https://github.com/broadinstitu…
matren395 Sep 6, 2023
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32 changes: 16 additions & 16 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,13 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
- name: Setup Python 3.8
uses: actions/setup-python@v2
uses: actions/checkout@v3
- name: Setup Python 3.11
uses: actions/setup-python@v4
with:
python-version: 3.8
python-version: 3.11
- name: Use pip cache
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ hashFiles('**/requirements*.txt') }}
Expand Down Expand Up @@ -44,13 +44,13 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
- name: Setup Python 3.8
uses: actions/setup-python@v1
uses: actions/checkout@v3
- name: Setup Python 3.11
uses: actions/setup-python@v4
with:
python-version: 3.8
python-version: 3.11
- name: Use pip cache
uses: actions/cache@v1
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ hashFiles('**/requirements*.txt') }}
Expand Down Expand Up @@ -98,21 +98,21 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout gnomad_methods
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
path: gnomad_methods
- name: Checkout gnomad_qc
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: recursive
repository: broadinstitute/gnomad_qc
path: gnomad_qc
- name: Setup Python 3.8
uses: actions/setup-python@v2
- name: Setup Python 3.11
uses: actions/setup-python@v4
with:
python-version: 3.8
python-version: 3.11
- name: Use pip cache
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ hashFiles('gnomad_methods/**/requirements*.txt') }}
Expand Down
10 changes: 5 additions & 5 deletions .github/workflows/publish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Validate version
run: |
package_version=$(grep 'version' setup.py | sed -E 's|.*([0-9]+\.[0-9]+\.[0-9]+).*|\1|')
Expand All @@ -19,12 +19,12 @@ jobs:
echo "Tag version (${tag_version}) does not match package version (${package_version})"
exit 1
fi
- name: Setup Python 3.8
uses: actions/setup-python@v2
- name: Setup Python 3.11
uses: actions/setup-python@v4
with:
python-version: 3.8
python-version: 3.11
- name: Use pip cache
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ hashFiles('**/requirements*.txt') }}
Expand Down
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ repos:
- id: end-of-file-fixer
- id: trailing-whitespace
- repo: https://github.com/psf/black
rev: 22.10.0 # This should be kept in sync with the version in requirements-dev.in
rev: 23.7.0 # This should be kept in sync with the version in requirements-dev.in
hooks:
- id: black
language_version: python3
Expand Down
8 changes: 4 additions & 4 deletions docs/requirements.docs.in
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
myst-parser==0.14.0
myst-parser
requests
Sphinx>=2.1,<3
sphinx-autodoc-typehints==1.10.3
Sphinx>=4.2.0,<7.0.0
sphinx-autodoc-typehints
sphinx-rtd-theme
Jinja2==3.0.3
Jinja2
58 changes: 29 additions & 29 deletions docs/requirements.docs.txt
Original file line number Diff line number Diff line change
@@ -1,20 +1,18 @@
#
# This file is autogenerated by pip-compile with python 3.8
# To update, run:
# This file is autogenerated by pip-compile with Python 3.11
# by the following command:
#
# pip-compile docs/requirements.docs.in
#
alabaster==0.7.13
# via sphinx
attrs==21.4.0
# via markdown-it-py
babel==2.12.1
# via sphinx
certifi==2022.12.7
certifi==2023.7.22
# via requests
charset-normalizer==3.1.0
charset-normalizer==3.2.0
# via requests
docutils==0.17.1
docutils==0.18.1
# via
# myst-parser
# sphinx
Expand All @@ -23,62 +21,64 @@ idna==3.4
# via requests
imagesize==1.4.1
# via sphinx
jinja2==3.0.3
jinja2==3.1.2
# via
# -r docs/requirements.docs.in
# myst-parser
# sphinx
markdown-it-py==1.1.0
markdown-it-py==3.0.0
# via
# mdit-py-plugins
# myst-parser
markupsafe==2.1.2
markupsafe==2.1.3
# via jinja2
mdit-py-plugins==0.2.8
mdit-py-plugins==0.4.0
# via myst-parser
myst-parser==0.14.0
mdurl==0.1.2
# via markdown-it-py
myst-parser==2.0.0
# via -r docs/requirements.docs.in
packaging==23.0
packaging==23.1
# via sphinx
pygments==2.14.0
pygments==2.16.1
# via sphinx
pytz==2023.3
# via babel
pyyaml==6.0
pyyaml==6.0.1
# via myst-parser
requests==2.31.0
# via
# -r docs/requirements.docs.in
# sphinx
snowballstemmer==2.2.0
# via sphinx
sphinx==2.4.5
sphinx==6.2.1
# via
# -r docs/requirements.docs.in
# myst-parser
# sphinx-autodoc-typehints
# sphinx-rtd-theme
# sphinxcontrib-applehelp
# sphinxcontrib-devhelp
# sphinxcontrib-htmlhelp
# sphinxcontrib-jquery
sphinx-autodoc-typehints==1.10.3
# sphinxcontrib-qthelp
# sphinxcontrib-serializinghtml
sphinx-autodoc-typehints==1.23.0
# via -r docs/requirements.docs.in
sphinx-rtd-theme==1.2.0
sphinx-rtd-theme==1.2.2
# via -r docs/requirements.docs.in
sphinxcontrib-applehelp==1.0.4
sphinxcontrib-applehelp==1.0.7
# via sphinx
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-devhelp==1.0.5
# via sphinx
sphinxcontrib-htmlhelp==2.0.1
sphinxcontrib-htmlhelp==2.0.4
# via sphinx
sphinxcontrib-jquery==4.1
# via sphinx-rtd-theme
sphinxcontrib-jsmath==1.0.1
# via sphinx
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-qthelp==1.0.6
# via sphinx
sphinxcontrib-serializinghtml==1.1.5
sphinxcontrib-serializinghtml==1.1.8
# via sphinx
urllib3==1.26.15
urllib3==2.0.4
# via requests

# The following packages are considered to be unsafe in a requirements file:
# setuptools
6 changes: 3 additions & 3 deletions gnomad/assessment/validity_checks.py
Original file line number Diff line number Diff line change
Expand Up @@ -180,9 +180,9 @@ def make_group_sum_expr_dict(
else:
logger.warning("%s is not in table's info field", field)

annot_dict[
f"sum{delimiter}{field_prefix}{group}{delimiter}{sum_group}"
] = hl.sum(sum_group_exprs)
annot_dict[f"sum{delimiter}{field_prefix}{group}{delimiter}{sum_group}"] = (
hl.sum(sum_group_exprs)
)

# If metric_first_field is True, metric is AC, subset is tgp, sum_group is pop, and group is adj, then the values below are:
# check_field_left = "AC-tgp-adj"
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