Develop#273
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…pend sample_trinucs returns the center (mutated) position, but the trinuc slice was starting at that position rather than one before it, so trinuc[1] was the 3' context base instead of the ref base. generate_snv uses trinuc[1] as the ref base for transition-matrix lookup and REF==ALT zeroing, so the wrong base was being consulted — Keshav's zeroing fix in #267 only worked when reference[pos] == reference[pos+1]. Fix: shift the slice to reference[local_location-1: local_location+2] so trinuc[0]=5' flank, trinuc[1]=ref base, trinuc[2]=3' flank. Also remove the dead self.all_ins.append(temp_snv) in generate_snv; SNVs were being accumulated in MutationModel.all_ins (a list that is never read) rather than nowhere, a copy-paste artifact from generate_deletion. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
These lists were never read anywhere; ContigVariants has its own independent all_ins/all_dels used for overlap detection. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Fix for memory leak
…to implement avg_seq_error in such a way that actually affects the output.
The main loop used <= instead of < causing num_errors+1 errors to be collected. The fallback loop called rng.choice(quality_scores) which returns a score value, not an index, making quality_scores[index] wrong; replaced with rng.integers(len(quality_scores)). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ures - Add num_errors argument to all get_sequencing_errors() calls - Change reference_segment from SeqRecord to Seq in error model tests - Add errors_per_read argument to generate_reads() calls - Add num_errors argument to finalize_read_and_write() calls - Add errors_per_read argument to read_simulator_single() calls - Remove now-unused SeqRecord imports from test_error_and_mut_models and test_seq_error Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Fix fallback loop in get_sequencing_errors: use <= median so uniform quality arrays (all scores equal) always make progress. New tests: - test_sem_num_errors_zero_produces_no_errors - test_sem_num_errors_caps_output - test_sem_fallback_loop_fills_errors_with_uniform_high_quality - test_finalize_read_and_write_returns_error_count - test_errors_per_contig_proportional_to_contig_length - test_errors_per_contig_zero_for_zero_coverage Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Fix blacklist range to exclude the deletion anchor so deletions don't remove themselves during the cleanup pass - Fix quality array concatenation to use dtype=int so deletion errors (which produce an empty quality slice) don't promote the array to float64 and break the chr() call in finalize_read_and_write - Remove dead num_errors capture from finalize_read_and_write return value - Add tests for indel error paths, errors_per_read gate logic, and score clamping in TraditionalQualityModel Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Error improvements
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…rective Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
keshav-gandhi
approved these changes
May 3, 2026
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Changes to be included in NEAT 4.4.1 (bug fixes and opitimizations for NEAT 4.4)