Dev - #4918

Merged

hanars merged 182 commits into

Aug 7, 2025

Commits on Jul 15, 2025

add key to saved variant model
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c17c75b
intial command
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Merge branch 'clickhouse-variant-lookup' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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updates for all dataset types
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find usages that need updating
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a0566a0
backend specific reloading logic
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f335375
clickhouse genotype helper
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e039cac

Commits on Jul 16, 2025

correctly set sample data
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b1f8bc6
fix create saved variant
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f0a40b3
better todos;
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8cc5e42
cleanup and add genome version to helpers
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b5d3b2e
add datset type
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1d09d68
return saved variants with annotations
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676f3e7
fix bulk create tags behavior
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2c17998
variant genes from clickhouse
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f3ec231
filter saved variants by clickhouse genes
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da202d0
variant gene note id
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53b9910

Commits on Jul 17, 2025

Commits on Jul 18, 2025

add id mapping logic for SVs
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0f9f5f8
remap gcnv based on callset ids
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bda4430
whitelist known dropped svs
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3893df5
better sv mapping
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37802ba

Commits on Jul 21, 2025

more sv remapping
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sv remapping ctd
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647638c

Commits on Jul 22, 2025

sv remapping
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Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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c40fe6d
ghroup by variant id
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35336f2
more remapping
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98e49d8

Commits on Jul 23, 2025

misc updates
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550d0c6
update report saved variant json
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68ab372
sv remapping
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932269e
fix typo
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f97603e
report test fixes
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b8fbb2b
fix project context
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03c3c80
fix test
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68caf15
Merge branch 'clickhouse-unit-test' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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cf6a070
remove default for clickhouse
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7207ef8
add missing case
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c13e82f
clean up
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1a60b48
TODOs
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3aa184f
sv remapping
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c17cba6
remove deprecated lift finctionality and clean up variant search calls
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8cc4882
clean up
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339c544

Commits on Jul 24, 2025

Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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6e8e74a
sv remapping
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dc3c4b9
sv remapping
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36e7f69
fix saved variant parsing
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dba314c
finalize set key command
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4c65f54
correctly get genes for bulk created variants
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9cca269

Commits on Jul 25, 2025

correclt set variant load and reload logic for bulk create saved variants
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a6db828
oops
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0e908f5
Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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d2443b5
fixture data for clcikhosue saved variants
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f146d17
fix lookup for saved variants with no key
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a3e39b7
properly set joined annotations for annotation only query
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0256415
fix annotation joins
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4c43495
transcript fixture data
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e1da17f
add clickhouse to test fixtures
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1cdcc21
updo overzealous fixtures
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b6c3b4c

Commits on Jul 28, 2025

fix clickhouse report queries
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bd498c7
fix fixture data
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393c887
handle multiple discovery saved variants with same key
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f24f5ec
handle multiple discovery saved variants with same key
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f81b549
handle no discovery gene
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1190fec
conditionally mock backend for aip test
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8250d30
clean up
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1a9ff1c
fix bulk tags
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1bbfc96
test daip tags different in different backends
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1be2bb5
use correct genome version for tags
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ed1772d
spilt fixtures
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de707b5
clean up saved variant json
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4ebde1d
codacy
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create saved variant test
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edc329f

Commits on Jul 29, 2025

fix underlying clinvar join
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cb668e3
fix save sv test
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7bc6b3b
fix tests
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cc05c1b
fix transaction rollbacks
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80f545c
codacy fixes
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9d1e959
more transaction cleanup
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49fcf56
fix fixtures
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ba5770e
restrict tests to needed databases
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9ba3e6b
Revert "fix fixtures"
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fix report fixtures
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more transactin clean up
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2b15fe4
fix report fixture data
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a91a688
test clinvar in metadata
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b3e6c1f
fix report tests
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7964b6e
more test db cleanup
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f53f342
fix reload clinvar test dbs
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b52e336
transaction support mixin
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b25af06
deprecate utils test
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fix tranasaction support
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c468a5f
Revert "fix tranasaction support"
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27aec5e
fix variant search tests
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fix test
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397fce1
correct success file for clickhouse loading
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859da8e
Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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7f6717b

Commits on Jul 30, 2025

fix transaction cleanup
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a2055f6
test fixes
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fb2f10a
properly configure clickhouse vs hail for reload testing
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e3a727b
fix missing import
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40426d6
actually test clickhouse for check new samples
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aaaecec
check samples reload logs
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d701db3
fix response test
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1ed36d3
check smaples test cleanup
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59a6ff4
actually cover genotype updates
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8453e9b
clear non transaction databases at end of test class
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9c14ee5
fix variant search tests
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b518d79
syntax cleanup
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fix gregor metadta test
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codacy
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fix family discovery tags;
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relioad dictionary
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0683887
fix typo
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229f8b9
reload for every test
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855761e
fir search test dictionary reloading
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22ca944
test coverage audit
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7cb1003
disable reload variants
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addaa2c
test save clickhouse gene note with selected transcript
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5d9103f
remove todos
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e910c8c
test set keys
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ebdcd23
test metadata for other dataset types
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ac5d68e
actually test clcikhsoue report svs
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e78b3ae
fix test
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3a7ce83

Commits on Jul 31, 2025

manage command test coverage
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Merge branch 'clickhouse-saved-variants' of https://github.com/broadinstitute/seqr into backend-specific-call-cleanup
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d9cf2f8
do not implement variant ids lookup
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implement clickhouse get single variant
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e4fb9eb
test query single variant
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ca00bf7
test clickhouse get single variant
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92983d0
codacy
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0cfa9f4
fix tests
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df1ed81
fix delete family note bug
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bf72f7d
Merge pull request #4901 from broadinstitute/delete-analysis-note-bug
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bccd0fe
correctly allow for external anvil family deletion
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b117dc4
Merge pull request #4902 from broadinstitute/anvil-user-delete-family
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a08795d

Commits on Aug 1, 2025

Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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e327de5
pr feedback
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d6319f8
mosc fixes for dev deployment
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c758c38
fix sample type casing
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bdf814b
Merge pull request #4903 from broadinstitute/clcikhosue-deploy-fixes
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1f4f27a
fixture data
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636c5c5
implement hom alt trans del override
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eb8f3cc
test comp het trans deletion
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f5aabbf
actually test gene counts in clickhouse tests
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6108efb
Merge branch 'dev' of https://github.com/broadinstitute/seqr into comp-het-trans-deletion
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8173f4f
fix new seqr pop
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e76df7c
Merge pull request #4905 from broadinstitute/clickhouse-gene-count-unit-tests
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554b534
fix test redis setup
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49e411c
Merge pull request #4906 from broadinstitute/test-redis-cleanup
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d3a00c7
Merge pull request #4899 from broadinstitute/backend-specific-call-cleanup
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Merge branch 'dev' of https://github.com/broadinstitute/seqr into clickhouse-saved-variants
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38ce601
Merge branch 'dev' of https://github.com/broadinstitute/seqr into comp-het-trans-deletion
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f40d488
Merge pull request #4890 from broadinstitute/clickhouse-saved-variants
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1a47f5a
Merge branch 'dev' of https://github.com/broadinstitute/seqr into comp-het-trans-deletion
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bb0c617

Commits on Aug 4, 2025

use keywrord args instead of dicts
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79217b3
add tests for standard searches
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cedcffa
standard search tests pass
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Merge pull request #4907 from broadinstitute/sv-search-clinvar-bug
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ffe8f19
add allele validation before querying VLM
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be5066b
Merge pull request #4904 from broadinstitute/comp-het-trans-deletion
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2c55b85
Merge pull request #4909 from broadinstitute/better-lookup-variant-validation
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c1228b3
fix json encoding for gsvs with null genes
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8819763
fix test
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da95a43
Merge pull request #4910 from broadinstitute/missing-sv-gene-null-encoding
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2ddd697

Commits on Aug 5, 2025

restrict no location searches in clickhouse
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d44ffd0
correctly validate multiple sample types per family
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update saved searches
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remove sv callset af from ui
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Merge pull request #4914 from broadinstitute/no-location-search-validation
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Merge pull request #4915 from broadinstitute/deprecate-sv-callset-af
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2729f2f

Commits on Aug 6, 2025

migrate from rocksdb to join tables
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lint
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0ff686a
remove unused
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clean up unused abstract base classes
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fix deleted clickhouse model routing
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f986cd8
cleaner clcikhosue migration routing
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5dcae64
fix fistrue loading for new join tables
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48bab4b
better comment
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Merge pull request #4916 from broadinstitute/benb/join_table_non_snv_indel
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958c874

Commits on Aug 7, 2025

bump changelog
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