Fix probability_rates mismatch with local_mut_regions in generate_var…#262
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joshfactorial merged 2 commits intoApr 18, 2026
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…iants probability_rates was computed from the full mutation_rate_regions array before intersecting with the current block. intersect_regions can return a different number of entries (e.g., a sub-block falling entirely within one region returns 1 entry regardless of how many regions exist), so passing the original probability_rates to rng.choice caused a numpy ValueError when lengths differed. Fix: compute probability weights from local_mut_regions after intersection, replacing any None rates (no mutation BED supplied) with the model's average mutation rate. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…n tests The probability_rates fix (previous commit) was incomplete because intersect_regions had two related bugs that caused crashes regardless: 1. Middle regions dropped: the original algorithm only matched regions containing block_start or block_end, so any region fully inside the block was silently skipped. 2. Zero-length fallback: when block_end == last_region_end (always the case in practice after recalibrate_mutation_regions), the condition `block_end < region[1]` was False, so a zero-length entry (last_end, block_end, default) was appended, triggering "Invalid Mutation Region" → ValueError immediately after. Fix: rewrite intersect_regions using overlap arithmetic (max/min clipping) so every region that overlaps the block is included and the tail fallback only fires when the block genuinely extends past all regions. Also substitutes None rates in the pre-loop factors calculation (generate_variants.py line 81) to prevent TypeError when mutation_rate_regions contains None entries from recalibrate_mutation_regions. Adds tests/test_read_simulator/test_generate_variants.py with 15 regression tests covering: intersect_regions with 3/4 regions, block_end == last_region_end, partial overlaps, contiguity, full coverage, outside-all-regions fallback; generate_variants with 2/3/4 regions, None rates, correctness checks. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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…iants
probability_rates was computed from the full mutation_rate_regions array before intersecting with the current block. intersect_regions can return a different number of entries (e.g., a sub-block falling entirely within one region returns 1 entry regardless of how many regions exist), so passing the original probability_rates to rng.choice caused a numpy ValueError when lengths differed.
Fix: compute probability weights from local_mut_regions after intersection, replacing any None rates (no mutation BED supplied) with the model's average mutation rate.