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varfish-org / varfish-server-worker

Rust-based background worker for varfish-server
MIT License
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feat: inhouse freqs useable in seqvars query (#232) #522

Closed holtgrewe closed 3 weeks ago

holtgrewe commented 3 weeks ago

Summary by CodeRabbit

coderabbitai[bot] commented 3 weeks ago

[!CAUTION]

Review failed

The pull request is closed.

Walkthrough

The changes in this pull request involve modifications to several files, primarily focusing on enhancing the handling of large files through Git LFS, updating JSON configurations for genomic data, and refining the functionality of query processing in the seqvars module. New entries for LFS tracking have been added, along with structural changes to JSON files to improve organization and clarity. Additionally, the run function and query handling have been updated to incorporate in-house frequency data, enriching the querying capabilities of the application.

Changes

File Path Change Summary
.gitattributes Added entries for LFS tracking for tests/seqvars/query/db-dynamic/** and tests/strucvars/query/db-dynamic/**.
src/seqvars/aggregate/mod.rs Modified run function to include genome release name in RocksDB metadata.
src/seqvars/query/interpreter/frequency.rs Enhanced passes function with additional checks for inhouse frequency filter.
src/seqvars/query/mod.rs Added optional path_inhouse_db argument and updated run_query to accept inhouse parameter. Introduced inhouse module.
tests/seqvars/query/Case_1.query.json Restructured JSON format for improved organization, including new objects for genotype and frequency.
tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/paths.txt New file added with metadata, tracked by Git LFS.
tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/*.sst Multiple new binary files added, tracked by Git LFS.
tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/* New files added for RocksDB management, including CURRENT, IDENTITY, LOG, MANIFEST, and OPTIONS.
tests/seqvars/query/dragen.query.json Modified JSON structure to enhance organization, including new sections for genotype, quality, and frequency.

Poem

In the burrow deep, we make our play,
With files and data, we hop all day.
Large files tracked with care and grace,
New paths and queries in our space.
A world of genes we now explore,
With every change, we leap for more! 🐇✨

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codecov[bot] commented 3 weeks ago

Codecov Report

Attention: Patch coverage is 76.47059% with 44 lines in your changes missing coverage. Please review.

Project coverage is 79%. Comparing base (0ce7f13) to head (1b1a37f). Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/seqvars/query/interpreter/frequency.rs 39% 20 Missing :warning:
src/seqvars/query/mod.rs 87% 19 Missing :warning:
src/seqvars/aggregate/mod.rs 0% 5 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #522 +/- ## ====================================== + Coverage 71% 79% +7% ====================================== Files 43 43 Lines 11830 12012 +182 ====================================== + Hits 8510 9492 +982 + Misses 3320 2520 -800 ``` | [Files with missing lines](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/522?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org) | Coverage Δ | | |---|---|---| | [src/seqvars/aggregate/mod.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/522?src=pr&el=tree&filepath=src%2Fseqvars%2Faggregate%2Fmod.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvYWdncmVnYXRlL21vZC5ycw==) | `39% <0%> (-1%)` | :arrow_down: | | [src/seqvars/query/mod.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/522?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Fmod.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvbW9kLnJz) | `59% <87%> (+49%)` | :arrow_up: | | [src/seqvars/query/interpreter/frequency.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/522?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Finterpreter%2Ffrequency.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvaW50ZXJwcmV0ZXIvZnJlcXVlbmN5LnJz) | `71% <39%> (-14%)` | :arrow_down: | ... and [14 files with indirect coverage changes](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/522/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org)