fix overlapping condition of boundary of exon/intron #77
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Codecov Report
@@ Coverage Diff @@
## master #77 +/- ##
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+ Coverage 45.60% 45.66% +0.05%
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Files 16 16
Lines 2004 2006 +2
Branches 64 65 +1
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+ Hits 914 916 +2
+ Misses 1026 1025 -1
- Partials 64 65 +1
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nokara26
commented
Jun 6, 2023
| @@ -26,8 +26,10 @@ | |||
| d (Math/abs (- nref nalt))] | |||
| (when (and (not= 1 nref) (not= 1 nalt) | |||
| (some (fn [[s e]] | |||
| (or (<= pos s (+ pos nref -1)) | |||
| (<= pos e (+ pos nref -1)))) exon-ranges)) | |||
| (and (not= s e) | |||
There was a problem hiding this comment.
Usually s and e are different value.
But when calculate offset, s and e are same value and this sometimes causes Variants overlapping a boundary of exon/intron are unsupported error.
So I added (not= s e) condition.
varity/src/varity/vcf_to_hgvs/protein.clj
Lines 93 to 94 in a155c38
federkasten
approved these changes
Jun 26, 2023
| @@ -17,7 +17,8 @@ | |||
| 6 "XX" "X" [[2 4] [7 10]] | |||
| 6 "XXX" "X" [[2 4] [7 9]] | |||
| 3 "XXX" "X" [[2 3] [6 9]] | |||
| 1 "XXXXX" "X" [[4 7]]) | |||
| 1 "XXXXX" "X" [[4 7]] | |||
| 9 "XXX" "XXX" [[2 4] [8 11]]) | |||
There was a problem hiding this comment.
Including tests for cases where s equals e is recommended.
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I found
Variants overlapping a boundary of exon/intron are unsupported errorwhen mutation occur at termination codon.Then I fix boundary of exon/intron overlapping condition.