feat(count): add --reverse-complement to also match RC of guides#30
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werner291 wants to merge 1 commit into
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feat(count): add --reverse-complement to also match RC of guides#30werner291 wants to merge 1 commit into
werner291 wants to merge 1 commit into
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Stores guides under canonical form (lex-min of fwd, RC) and probes both orientations on lookup; reads resolving to different guides across orientations count as ambiguous. Palindromes collapse to one entry; canonical collisions across guides evict both. Off by default; output schema unchanged.
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Closes #19.
Adds
--reverse-complement/-rtoguide-counter countfor assays whose sequencing primer reads the antisense strand. Off by default; output schema unchanged.Each guide is stored under its canonical form (lex-min of fwd and RC), keeping the lookup the same size as forward-only. Each read window is then looked up under both its forward and reverse-complement forms; if the two probes return different guides, the read counts as ambiguous (
None), otherwise the matching guide wins. (One probe isn't enough because a 1-mismatch hit can live in the 1-mm neighbourhood of either orientation, not just canonical.) Palindromes collapse to one entry; canonical collisions across guides (fwd_A == rc(fwd_B)) evict both. Windows with non-ACGT bytes skip the RC probe.One asymmetry: in forward-only mode, an exact match beats a 1-mismatch via insertion order. In RC mode, an exact fwd-orientation hit on guide A and a 1-mismatch rc-orientation hit on guide B resolve as ambiguous (
None) rather than letting the exact win. Internally consistent, slight sensitivity loss vs. forward-only; happy to add an exact-beats-mismatch tiebreak across orientations if you'd prefer.The matching logic has a few subtle cases (palindromic guides; reads that could plausibly belong to two different guides once you allow a one-base mismatch). I worked through each and added regression tests, but maintainer eyes on the algorithm would be welcome.
Open question
Whether to add a strand-aware count column. The issue does not ask for it and it would break consumers of
*.counts.txt, so v1 keeps the schema; happy to follow up.