Add extension conditional branch to insertion #119
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nokara26
commented
Feb 6, 2025
| "chr1" 26773690 "C" "CGCAGCA" {:prefer-insertion? true} '("p.Q1334_R1335insQQ") | ||
| ;; prefer-insertion? | ||
| "chr1" 26773690 "C" "CGCAGCA" {:prefer-insertion? true} '("p.Q1334_R1335insQQ") ;; not actual example (+) | ||
| "chr10" 103089678 "T" "TTCC" {:prefer-insertion? true} '("p.*562Eext*1") ;; not actual example (-) |
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master branch return value: '("p.E561_*562insE")
nokara26
commented
Feb 6, 2025
| (and (some? unit) (= ref-repeat 1) (= alt-repeat 2)) :duplication | ||
| (and (some? unit) (pos? alt-repeat)) :repeated-seqs | ||
| (and (pos? nprefo) (zero? npalto)) :deletion | ||
| (and (pos? nprefo) (pos? npalto)) (if (= base-ppos 1) | ||
| :extension | ||
| :indel) | ||
| (and (zero? nprefo) (pos? npalto)) :insertion | ||
| (and (zero? nprefo) (pos? npalto)) (if first-diff-aa-is-ter-site |
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first-diff-aa-is-ter-site is boolean and true when first changed codon is stop codon.
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I added extension branch to insertion.