feat: stochastic resolution of IUPAC ambiguity codes in reference gen…#136
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…omes IUPAC codes (R/Y/M/K/S/W/H/B/V/D) in reference FASTAs were previously silently mapped to N, producing excess-N reads indistinguishable from assembly gaps. gen-reads now resolves each code to one of its constituent bases at reference-load time using the per-contig seeded RNG, making results reproducible while avoiding systematic reference bias. FastaStream now yields raw sequence strings; resolve_iupac_bases() in common::file_tools::fasta_stream performs the stochastic conversion. gen-mut-model and gen-gc-bias-model continue using simple Nucleotide::from conversion (IUPAC → N), appropriate for model-building from real VCF data. Bumps version to 1.5.2. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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…omes
IUPAC codes (R/Y/M/K/S/W/H/B/V/D) in reference FASTAs were previously silently mapped to N, producing excess-N reads indistinguishable from assembly gaps. gen-reads now resolves each code to one of its constituent bases at reference-load time using the per-contig seeded RNG, making results reproducible while avoiding systematic reference bias.
FastaStream now yields raw sequence strings; resolve_iupac_bases() in common::file_tools::fasta_stream performs the stochastic conversion. gen-mut-model and gen-gc-bias-model continue using simple Nucleotide::from conversion (IUPAC → N), appropriate for model-building from real VCF data.
Bumps version to 1.5.2.