[TEST] #68: phraya plan CLI acceptance tests

[crashfrog]

Summary

• Add comprehensive integration tests for phraya plan CLI command
• Tests cover all 4 use cases and error conditions
• All tests failing as expected (RED phase) pending implementation

Test Coverage

Acceptance Criteria Tested

• Parse command-line arguments (--inputs, --reference, --output)
• Read FASTA/FASTQ input files
• Compute k-mer sketches
• Detect use cases (Case 2/3/4)
• Compute k-mer uniqueness
• Generate task lists
• Write .phrayaplan files
• Log detected use case
• Error handling for invalid inputs
• Multi-file input support

Test Filter Command

cargo test --test integration_test_plan -- --ignored

All 10 tests currently FAIL as expected (feature not implemented).

API Surface Assumed by Tests

The tests assume a phraya plan CLI command with the following signature:

phraya plan \
  --inputs <file> [--inputs <file> ...] \
  [--reference <ref-file>] \
  --output <plan.phrayaplan>

Behavior:

• Reads sequence files (auto-detects FASTA/FASTQ, supports gzip)
• Creates Sequence objects for all inputs
• Computes minimizer sketches (k=21, w=11 default)
• Detects use case based on input composition:
  • Case 2: --reference + --inputs (reads) -> ReadsWithRef
  • Case 3: --inputs with mix (contigs + reads), no --reference -> ContigsWithReads
  • Case 4: --inputs (contigs only), no --reference -> ContigsOnly
• Computes k-mer uniqueness across all sequences
• Generates task list (query_id, target_id pairs) per use case
• Writes binary MessagePack + zstd PhrayaPlan to output file
• Logs detected use case to stderr (e.g., "Detected Case 2: reads with reference")
• Exits with code 0 on success, non-zero on error
• Provides clear error messages on file I/O failures or missing arguments

Task List Generation:

• Case 2: One task per read, target=reference (index 0)
• Case 3: Tasks depend on centroid selection (not fully specified in test)
• Case 4: All-vs-all tasks (M*(M-1)/2)

Generated files are validated by reading them back using phraya_io::plan::read_plan().

🤖 Generated with Claude Code