broadinstitute / viral-classify / 20394768678

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Add deplete_minimap2_bam for minimap2-based read depletion

Implement a new depletion method using the Minimap2.idxstats() method
from viral-core to identify and remove reads matching reference databases.

- Add deplete_minimap2_bam function using PAF-based minimap2 alignment
- Add CLI parser and main function following existing depletion patterns
- Add unit tests for basic depletion, empty input, and empty output cases
- Uses multi_db_deplete_bam helper for multiple reference database support

The implementation follows the established patterns from deplete_blastn_bam,
deplete_bmtagger_bam, and deplete_bwa_bam.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

238 of 405 branches covered (58.77%)

Branch coverage included in aggregate %.

1624 of 2441 relevant lines covered (66.53%)

0.67 hits per line