Auto Strategy Decision Logic

[crashfrog]

Parent

Part of generalized allelic typing system design (discussed in conversation 2026-05-22)

What to build

Implement --strategy auto that analyzes input characteristics and selects fast/balanced/sensitive automatically. Decision happens before workflow execution (pre-analysis, not adaptive mid-workflow).

Decision logic:

• Detect input type from sequence statistics
• Contigs (mean length >1000bp, N50 high) → select "fast"
• Reads (mean length <500bp) → select "balanced"
• Edge cases or uncertain → default "balanced"

Add decision rationale to output notes field: {auto_decision: "contigs detected, selected fast strategy"}.

This is a CLI-level feature that picks one of the three workflows and executes it once.

Acceptance criteria

• --strategy auto option works in CLI
• Pre-analysis inspects input sequences (type, length distribution, N50)
• Correctly routes to fast/balanced/sensitive based on characteristics
• Decision rationale included in workflow output notes
• Tests verify decision logic for contigs, reads, edge cases
• Help text documents auto strategy behavior

Blocked by

#58 - CLI Strategy Routing

[crashfrog]

Completed in PR #82 - implemented auto strategy that analyzes sequence characteristics (length, N50) and automatically selects fast/balanced/sensitive strategy. Includes FileReaderWithPath wrapper for preserving file paths through compression.