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Optional per-read scoring parameters (abpoa_para_t.read_abpt) - #13
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glennhickey wants to merge 3 commits into
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A caller aligning reads of mixed divergence in one abpoa_msa() call can set read_abpt[i] to the parameters that should score read i against the graph. Only the sequence-to-graph alignment uses them; graph building, read order and output keep using the call's own parameters. NULL (the default from abpoa_init_para) leaves every read scored as before. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…oring parameters (abpoa_para_t.read_abpt), on v1.5.7 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Adds an optional
abpoa_para_t.read_abpt: an array ofabpoa_para_t *, one per read, so a caller can score each read against the graph with its own parameters (substitution matrix, gap penalties). If the array is NULL, or a read's entry is, that read uses the shared parameters. So abPOA behaves exactly as before unless a caller sets it.cactus uses it for per-row scoring in bar: each genome's row is aligned with the model for its divergence. ComparativeGenomicsToolkit/cactus#2024 pins this branch.
Changes:
read_abptadded toabpoa_para_t(in both copies ofabpoa.h), and set to NULL inabpoa_init_para.abpoa_anchor_poaandabpoa_poaalign each read with its own parameters, including the reverse-complement threshold.History: the branch is the original commit on v1.5.6, merged into
ai-optimization(where it had to fit the packed DP rows), then intomain(v1.5.7). Againstmainthe diff is just those three files.Testing on this branch:
read_abptunset, the CLI output is byte-identical tomain's overtest_data: 5 inputs × 13 option sets, 65 runs. The options cover alignment modes, result modes, scoring, convex gaps, banding, consensus, progressive, ambiguous strand and seeding.read_abpt, in both progressive modes. Identical copies of the default parameters for every read give the default alignment, and a different model for one read changes it.🤖 Generated with Claude Code