Release 4.5.3 - #310
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joshfactorial
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Jun 8, 2026
joshfactorial
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- Handle IUPAC ambiguity codes in the reference (Deal with difficulties hg38 #291)
GRCh38 and other assemblies carry IUPAC ambiguity codes (R, Y, S, W, K, M, B, D, H, V). NEAT previously had no handling for them: - they survived reference load (convert_masking only neutralized non-ACGT bases when an N was also present in the segment, and skipped bases before the first N), and - a surviving code at a sequencing-error site hit NUC_IND[base] and raised KeyError, crashing the run. Fix: resolve ambiguity codes to a concrete base at reference load. - common: add IUPAC_CODES map + resolve_iupac_bases(), which replaces each code with one of the bases it represents using the run's seeded RNG (reproducible). Vectorized; the no-codes common case is a single scan, so genome-scale references aren't penalized. 'N' is left for its existing low-quality masking. - split_inputs: resolve right after the existing upper(), so every downstream consumer (reads, BAM, golden VCF, error/trinucleotide lookups) only ever sees A/C/G/T/N. Logs a warning with the count. - error_models: defense-in-depth — NUC_IND lookup now skips a non-ACGT base instead of raising, so nothing can crash even if a code slips through. Tests: resolver unit tests (every code, counts, reproducibility, N left alone, length preserved) and an end-to-end runner test on a reference containing all ten codes plus an N run, asserting FASTQ output is clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Bump version to 4.5.3 and add the ChangeLog entry for the IUPAC ambiguity-code handling fix. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Handle IUPAC ambiguity codes in the reference (#291)
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