broadinstitute / viral-classify / 20881107329

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Add KMA k-mer alignment tool integration

Adds KMA (k-mer alignment) tool wrapper following existing patterns from
kraken2 and kb-python for taxonomic classification of reads.

Implementation:
- classify/kma.py: Tool wrapper class inheriting from tools.Tool
  - version(): Parse version from kma -v output
  - build(): Wrapper for kma_index to build reference databases
  - classify(): Main classification method with BAM→FASTQ conversion
  - Handles empty BAM files with early return
  - Single/paired-end detection via file size comparison
  - Proper temp file cleanup in finally blocks

- metagenomics.py: CLI command registration
  - kma: Classify reads using KMA database
  - kma_build: Build KMA database from reference FASTA
  - Input validation for mismatched argument lists
  - Uses split_args=True pattern consistent with other tools

- requirements-conda.txt: Added kma>=1.4.0 dependency

- test/unit/test_tools_kma.py: Comprehensive unit tests
  - test_build_invokes_kma_index_with_expected_arguments
  - test_classify_single_end_from_bam
  - test_classify_paired_end_from_bam
  - test_classify_returns_early_when_bam_is_empty
  - All external dependencies properly mocked

- test/input/TestKMA/ref.fasta: Test input with 3 SARS-CoV sequences

- CLAUDE.md: Updated documentation with KMA commands and module info

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

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