Fix exon/intron boundary determine process and frameshift that affects initiation site #92
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #92 +/- ##
==========================================
+ Coverage 46.45% 46.93% +0.48%
==========================================
Files 16 16
Lines 2101 2124 +23
Branches 70 71 +1
==========================================
+ Hits 976 997 +21
- Misses 1055 1056 +1
- Partials 70 71 +1 ☔ View full report in Codecov by Sentry. |
nokara26
commented
Feb 1, 2024
| (if (= alt \*) | ||
| (cond | ||
| (or ref-include-utr-ini-site-boundary | ||
| (not (string/starts-with? alt-prot-seq "M"))) |
There was a problem hiding this comment.
To exclude UTR and initiation site is changed but first amino acid of alt-prot-seq is "M".
nokara26
commented
Feb 1, 2024
src/varity/vcf_to_hgvs/protein.clj
Outdated
| exon-ranges)))) | ||
| (let [[pos nref] (if (= (first ref) (first alt)) | ||
| [(inc pos) (dec nref)] | ||
| [pos nref])] |
There was a problem hiding this comment.
only check changed position
nokara26
force-pushed
the
fix/fix-exon-intron-overlap-and-ini-site-variant
branch
from
df0b6eb to
0587070
Compare
Refactor and generalize overlap-exon-intron-boundary?
federkasten
approved these changes
Feb 2, 2024
federkasten
deleted the
fix/fix-exon-intron-overlap-and-ini-site-variant
branch
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I fixed exon/intron boundary determine process to check position only changed.
And I fixed frameshift that affects initiation site.