broadinstitute / viral-core

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Build # 20857210908

Build Type

push

github

Committed by dpark01

Commit Message

Use batched SQLite queries for filter_bam_by_ids optimization

- Add add_from_readlist() method to ReadIdStore
- Add contains_batch() method for efficient batch membership checking
- Modify filter_bam_by_ids to buffer 50K reads and batch-query SQLite
- Add PERF logging for benchmarking

This reduces SQLite queries from N (one per read) to N/batch_size,
which should significantly reduce query overhead.

Run Details

36 of 47 new or added lines in 1 file covered. (76.6%)

4609 of 6536 relevant lines covered (70.52%)

0.71 hits per line