Dev - #5573

Merged

hanars merged 409 commits into

Sep 10, 2026

This pull request is big! We're only showing the most recent 250 commits

Commits on Aug 20, 2026

clean up
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7009f2e
fix test setup
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237145a
better scoping for new entry helpers
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cdd96e0
Merge branch 'depreacate-global-annotations-ht' of https://github.com/broadinstitute/seqr into depreacate-global-annotations-ht
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ruff
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ruff
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ruff
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ruff
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27f0f78
ruff
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1b5ffd1
updated vep mocking
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a7c3bbb

Commits on Aug 21, 2026

fix new sv test
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329e750
fix mito test fixture
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082984f
update assertion
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syntax fix
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46d359d
Merge branch 'depreacate-global-annotations-ht' of https://github.com/broadinstitute/seqr into depreacate-global-annotations-ht
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37fb831
test failures
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25db204
undo debug
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54e3d80
debug
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3797da4
initial copy all pipeline code
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5de4c68
merge gitignore
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2b61421
merge dockerignore
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775c6a9
update docker copy path
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0d3bd25
tweak readme
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da4d297
copyy cloudbuild yaml
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0d04860
unit tests
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dab03fb
release workflows
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3a7dc85
correct directory for unit test deps
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60c5a07
fix uv commands
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bd64115
correct ruff path
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84e8441
fix uv test
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e41da52
codacy ignore
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79254f5
fix codacy ignore
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b9f0467
run test in root dir
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052c99d
fi uv sync
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43f5fec
fix uv commands
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fd6dae4
iter test runner
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49b44c4
iter test runner
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ad41676
configure uv workspace
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de0f912
iter test runner
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375e13a
iter test runner
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d7cbf54
iter test runner
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cf0c510
iter test approach
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a71e9d3
iter command
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985959e
reset test command
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820e133
fix test command
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44df393
Potential fix for pull request finding 'CodeQL / Workflow does not contain permissions'

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github-advanced-security[bot]
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59a9548
plan test migration
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da20af3
add pytest django and clean up iimports to separate clickhouse migratios from rest of app
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bdf2798
add tests ettings module
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7dcb6b1
clean up seqr dependencies and add stub application
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fb68792
fix dict relaod behavior
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350f248
comment clean up
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1e643b6
django based test case
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3934d2c
plan update
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3c052d1
existing test cleanup
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0a4e1fc
first opass refatcor test clcikhouse
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ca83995
fix ruff
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d7ae384
add missed files
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a688ce7
fix ruff
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d93e20b
ruff and cleanup
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ab48f08
missing init
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e3e5cef
clean up
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060ba50
test config setup
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f432a5c
fix detail parquuet fixture
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26d1549
fix setup
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d6c8e1c
add missing file
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334c9b4
skip tests
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6744ddb
new plan
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3f6946b
restore files
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68883d7
fix fixtures
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6a225f6
fix field names
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ef89a90
misc test cleanup
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e03b26e
test cleanup and fix
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38f4c31
ruff
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0142d0b
ruff
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c866eb3
intermediate test iter
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aabe8e6
test reqrite
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4f056e4
remove plan
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eb178dd
unit test fix iter
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254100b
test fixes
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6688547
fix tests
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7edea85
ruff
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b4793f6
fix tests
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5b1ece8
test cleanup
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54a7c6c
fix tests
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c9a9bc8
test cleanup
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127adc3
test cleanup
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45cef52
fix tests
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73b02fb
ruff
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93778a5
remove redundant test
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56aa3d5
remove unneeded schema
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aae2cab
fix test
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f432f4b
Revert "remove unneeded schema"
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c5cb58c
fix test
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3c43437
fix test
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90c780d
ruff
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fix test
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c321e7c
fix test
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dce7fbf
fix test
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c1556ba
Revert "skip tests"
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18c7feb
remove debug
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789a2bc
reenable codacy for pipeline
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c9cc6c8
quote in bash scripts
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8b33e20
disable errors
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4c64fe6
more disable rules
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11dccc6
more disable rules
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1a7e9ab
codacy clean up
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fa9f7ac
remove deprecated param
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fe537b2
disable codacy errors
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4a22820
disable codacy errors
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9434caf
disable codacy errors
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30d1650
debug
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0d78f5e
Merge branch 'pipeline-codacy' of https://github.com/broadinstitute/seqr into deprecate-pipeline-migrations
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4508338
Merge branch 'deprecate-pipeline-migrations' of https://github.com/broadinstitute/seqr into better-new-variant-tests
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7904be2
actually delete the migrations!
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599028a
Merge branch 'deprecate-pipeline-migrations' of https://github.com/broadinstitute/seqr into better-new-variant-tests
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e7e5c34
undo debug
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d4f4d26
fix tests
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3cf100f
undo debug
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9fd72e4
debug
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0e55c84
fix filter
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d9b1237
fix test
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46d02dd

Commits on Aug 23, 2026

better mock table
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b25192f
debug
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49e7ba9
undo debug
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6c125dd
usable mito fixture data
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9986608
valid version for modified mt
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9110f9a

Commits on Aug 24, 2026

update fiel size test
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292b1f4
update new entries tests
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3355180
ruff
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Merge branch 'better-new-variant-tests' of https://github.com/broadinstitute/seqr into depreacate-global-annotations-ht
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efb8a19
fix mock paths
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4b2e5d2
update new variant tests
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2effd72
fix parquet locus parsing
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e8c7ea0
fix genome guild chrom prefix
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b1c1d93
fix tests
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5b730b3
fixy copy pasta
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666b394
fix new etries dependencies
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0e69033
handle missing max key
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2465481
use existing parquet for sv dedup
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25ddc4f
clean up
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ea888d2
ruff
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008bf39
misc fixes
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36d3301
fix helper test
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13b3a30
union type mismatch
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714a49e
fix xpos dt
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9d27c68
drop extra parquest cols
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dc95b25
ruff
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21aba8d
ruff
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3293ef5
fix gcnv fields
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e47e08c
type mismatch
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c6295f3
Merge branch 'depreacate-global-annotations-ht' of https://github.com/broadinstitute/seqr into remove-pipeline-enums
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81872db
clean up
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1cc7a06
type mismatch handling
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41ba2db
Apply suggestions from code review

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Copilot
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1926aab
debug
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e85161d
ruff
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aa24584
fix test
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cd316da
undo debug
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7390626
Merge branch 'depreacate-global-annotations-ht' of https://github.com/broadinstitute/seqr into remove-pipeline-enums
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6d193c1

Commits on Aug 31, 2026

PR feedback
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1e024a3
Merge branch 'pipeline-unit-test-django' of https://github.com/broadinstitute/seqr into pipeline-unit-test-django
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6a5c576
Merge branch 'pipeline-runner-to-seqr-repo' of https://github.com/broadinstitute/seqr into pipeline-unit-test-django
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8fab522
Merge branch 'pipeline-codacy' of https://github.com/broadinstitute/seqr into pipeline-codacy
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16a9fb4
Merge branch 'pipeline-unit-test-django' of https://github.com/broadinstitute/seqr into pipeline-codacy
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6d3fbca
Merge branch 'pipeline-codacy' of https://github.com/broadinstitute/seqr into deprecate-pipeline-migrations
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21c2388
Merge branch 'deprecate-pipeline-migrations' of https://github.com/broadinstitute/seqr into better-new-variant-tests
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df3f0f2
Merge branch 'better-new-variant-tests' of https://github.com/broadinstitute/seqr into depreacate-global-annotations-ht
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ef65082
Merge branch 'depreacate-global-annotations-ht' of https://github.com/broadinstitute/seqr into remove-pipeline-enums
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bf127a5
debug test failures
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5eaecd0
fix gcn test hail table
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76c451b
Revert "debug test failures"
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8c585ed
fix tests
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f00e583
debug test
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9d0b010
ruff
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d5fa95c
ruff
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c916850
ruff
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7b1170c
test fix
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celean up
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269fa52

Commits on Sep 1, 2026

remove unused function
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2303274
remove unused funcs
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704f11b
remove unused constants
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c1bc2ae
add missing consequence validation
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a659491
Merge branch 'remove-pipeline-enums' of https://github.com/broadinstitute/seqr into remove-unused-pipeline-funcs
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e6edec8
update comment
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4a871cd
remove unused HTs
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e8efef7
rewrite remap subset task for all projects
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b893af3
update parsing to actually work for multiple projects
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7c80597
updates to reading subsetted callset
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4564f6b
use updated single task
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1bf7c9e
use single callset for entries parquet
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0bf0bed
add more testing around exported entries
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ac056e0
ruff;
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77b232b
update diagram
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b1a149d
fix metadata global parsing
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b102188
annotate the global we actually want
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4bf06f8
update test;
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372b07f
ruff
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realistic counts
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fix hail syntax for task complete
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cb26b07
ruff
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Merge branch 'better-entries-test' of https://github.com/broadinstitute/seqr into single-project-subset-task
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058bec8
ruff
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Commits on Sep 2, 2026

Bump fast-uri from 3.1.5 to 3.1.7 in /ui
dependabot[bot]
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1a4eba1

Commits on Sep 3, 2026

Bump browserslist from 4.24.2 to 4.28.8 in /ui
dependabot[bot]
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87acaac
Merge pull request #5567 from broadinstitute/dependabot/npm_and_yarn/ui/fast-uri-3.1.7
hanars
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1b69f1b
Merge pull request #5568 from broadinstitute/dependabot/npm_and_yarn/ui/browserslist-4.28.8
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95fadae
update tests
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aefccd7
fix util tests
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525617e
debug
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436d6c1
fix tests
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b01ef40
Merge pull request #5555 from broadinstitute/depreacate-global-annotations-ht
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92ea7e2
fix test
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bcec49e
Merge branch 'dev' of https://github.com/broadinstitute/seqr into remove-pipeline-enums
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d949fbf
Merge branch 'remove-pipeline-enums' of https://github.com/broadinstitute/seqr into remove-unused-pipeline-funcs
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9df8305
rename task
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9f2cff4
split task logic
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565caec
Merge branch 'remove-pipeline-enums' of https://github.com/broadinstitute/seqr into single-project-subset-task
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448cbb5
debug
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24aa490
update ocs
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64daf44
explicitly separate out clcikhosue funcs
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65cec03
add dataproc retry
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938307d
test assertion order
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7f9e8cd
update tests
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4ec47f2
clean up
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d8fb9f7
Merge pull request #5564 from broadinstitute/remove-unused-pipeline-funcs
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de5b222
Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-loading-stability
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c45f34f
Merge branch 'dev' of https://github.com/broadinstitute/seqr into single-project-subset-task
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f9e8ed9

Commits on Sep 4, 2026

fix type checks
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1961aa9
fix index error
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fc9e158
Merge branch 'single-project-subset-task' of https://github.com/broadinstitute/seqr into single-project-subset-task
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a9334ad
use less memory intensive gt stats rebuild
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f89d923
clean up
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c471ea8
ruff
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79ff777

Commits on Sep 9, 2026

better back off strategy
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9ad154d
no delay on test retry
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bca4b4e
ruff
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59a66e7
fix ordered table create syntax
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4a4aa73
pr feedback
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9e41bf2
Revert "no delay on test retry"
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bf831a4
mock sleep
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e31670c
codacy
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0c6d891
setting override stability
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0120881
fix mock sleep

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Copilot
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01ff52e

Commits on Sep 10, 2026