return no-effect when ter site is inserted around ter site and fix extension determine process #115
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #115 +/- ##
==========================================
+ Coverage 46.93% 48.13% +1.19%
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Files 16 16
Lines 2124 2273 +149
Branches 71 72 +1
==========================================
+ Hits 997 1094 +97
- Misses 1056 1107 +51
- Partials 71 72 +1 ☔ View full report in Codecov by Sentry. |
nokara26
commented
Jan 20, 2025
| (if new-aa-pos | ||
| (coord/protein-coordinate new-aa-pos) | ||
| (coord/unknown-coordinate))))))) | ||
| :else |
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just change indent and move alt-prot-seq* let binding to line 581
| (let [alt-prot-seq* (format-alt-prot-seq seq-info)] | ||
| (cond | ||
| (and (not= ppos 1) | ||
| (ter-site-same-pos? ref-prot-seq alt-prot-seq*)) |
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change c-ter-adjusted-alt-prot-seq to alt-prot-seq*
nokara26
commented
Jan 20, 2025
| t (cond | ||
| ref-include-from-ter-start-and-over-ter-end :frame-shift | ||
| (and ref-include-from-ter-start-and-over-ter-end | ||
| (not first-diff-aa-is-ter-site)) :frame-shift |
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treat as extension when sequence is same until before ter site.
federkasten
reviewed
Jan 21, 2025
src/varity/vcf_to_hgvs/protein.clj
Outdated
Comment on lines
182
to
186
| (let [ref-ter-pos (count ref-prot-seq) | ||
| alt-ter-pos (inc (count (first (string/split alt-prot-seq #"\*"))))] | ||
| (and (string/includes? ref-prot-seq "*") | ||
| (string/includes? alt-prot-seq "*") | ||
| (= ref-ter-pos alt-ter-pos)))) |
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There is a possibility of a NullPointerException occurring.
Suggested change
| (let [ref-ter-pos (count ref-prot-seq) | |
| alt-ter-pos (inc (count (first (string/split alt-prot-seq #"\*"))))] | |
| (and (string/includes? ref-prot-seq "*") | |
| (string/includes? alt-prot-seq "*") | |
| (= ref-ter-pos alt-ter-pos)))) | |
| (and (string/includes? ref-prot-seq "*") | |
| (string/includes? alt-prot-seq "*") | |
| (let [ref-ter-pos (count ref-prot-seq) | |
| alt-ter-pos (inc (count (first (string/split alt-prot-seq #"\*"))))] | |
| (= ref-ter-pos alt-ter-pos)))) |
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federkasten
approved these changes
Jan 21, 2025
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I found
:clj-hgvs.coordinate/protein-coordinateerror when ter site is inserted around ter site and some extension varints are determined as frameshift.So I fixed protein-alteration type determine process.