Dev #3860
Dev #3860
Commits on Jan 23, 2024
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Merge pull request #3834 from broadinstitute/variant-lookup-desription
add help label for variant id in variant lookup
Commits on Jan 24, 2024
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Merge pull request #3835 from broadinstitute/enable-37-hail-backend
Enable build 37 for hail backend
Commits on Jan 25, 2024
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Merge pull request #3836 from broadinstitute/hal-spark-memory
explicitly set spark driver memory
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Merge branch 'dev' of https://github.com/broadinstitute/seqr into var…
…iant-lookup-genotypes
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Merge pull request #3838 from broadinstitute/str-env-var
parse env var to int
Commits on Jan 26, 2024
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Merge pull request #3839 from broadinstitute/hail-backend-test-init
add env variable to hail search tests
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fix: requirements.txt to reduce vulnerabilities
The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-6050294 - https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-6126975
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Merge pull request #3837 from broadinstitute/variant-lookup-genotypes
Use variant lookup page for all-project single variant search
Commits on Jan 30, 2024
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Bump aiohttp from 3.9.0 to 3.9.2 in /hail_search
Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.9.0 to 3.9.2. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](aio-libs/aiohttp@v3.9.0...v3.9.2) --- updated-dependencies: - dependency-name: aiohttp dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>
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Merge pull request #3841 from broadinstitute/dependabot/pip/hail_sear…
…ch/aiohttp-3.9.2 Bump aiohttp from 3.9.0 to 3.9.2 in /hail_search
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Merge pull request #3845 from broadinstitute/grch37-variant-search
properly handle 37 variant ids
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Merge pull request #3846 from broadinstitute/hail-backend-java-opts
configure hail backend extraJavaOptions
Commits on Jan 31, 2024
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Merge pull request #3840 from broadinstitute/snyk-fix-cdcd8fd93029db4…
…7ede7438ef3ba23a2 [Snyk] Security upgrade cryptography from 41.0.6 to 42.0.0
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Commits on Feb 1, 2024
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Merge pull request #3848 from broadinstitute/lookup-performance
refactor variant lookup aggregation
Commits on Feb 2, 2024
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Merge pull request #3849 from broadinstitute/lookup-optimization
do not load project tables with no queried variants
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Merge pull request #3852 from broadinstitute/cache-lookup
add caching for variant lookup
Commits on Feb 6, 2024
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Update indeterministic test in test_json_for_saved_variants_with_tags
The original code here does a next(iter(<dictionary>)) which has an indeterministic order, so this occasionally returns the variantTag for an AIP variant, which gets transformed with a different key, causing this test to intermittently fail. For this reason, we'll hard select the the variant VT1726961_2103343353_r0390_100 to look at the keys for.
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Bump cryptography from 41.0.6 to 42.0.0
Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.6 to 42.0.0. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@41.0.6...42.0.0) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>
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feat: Clearly show transcript labels in variant results when differen…
…t to default (cherry picked from commit 9d8ad2a)
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Merge pull request #3857 from broadinstitute/dependabot/pip/cryptogra…
…phy-42.0.0 Bump cryptography from 41.0.6 to 42.0.0
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Merge pull request #3856 from illusional/patch-2
Update indeterministic assertion in test_json_for_saved_variants_with_tags
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Merge pull request #3858 from bioinfomethods/feat-show-non-default-tr…
…anscript feat: Clearly show when variant transcript is not Canonical nor MANE
