Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Allow comma in mutation name when transcripts present #453

Merged
merged 3 commits into from
Oct 1, 2024
Merged

Allow comma in mutation name when transcripts present #453

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
d1541a0
allow comma in mutation name when transcripts present
bprize15 Oct 1, 2024
a14041e
add missing colon
bprize15 Oct 1, 2024
43ca3b8
rename transcripts to reference genomes
bprize15 Oct 1, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 22 additions & 1 deletion src/main/webapp/app/shared/util/firebase/firebase-utils.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -405,13 +405,34 @@ export const hasMultipleMutations = (mutationName: string) => {
};
export const isMutationEffectCuratable = (mutationName: string) => {
const multipleMuts = hasMultipleMutations(mutationName);
if (multipleMuts) {
if (multipleMuts && !areSameAlterationsWithDifferentReferenceGenomes(mutationName)) {
return false;
}
const excludedMutations = ['Oncogenic Mutations'];
return excludedMutations.filter(mutation => mutationName.toLowerCase().includes(mutation.toLowerCase())).length === 0;
};

function areSameAlterationsWithDifferentReferenceGenomes(mutationName: string) {
const alterations = mutationName.split(',');

if (alterations.length !== 2) {
return false;
}

const alt1 = alterations[0].trim().toLowerCase();
const alt2 = alterations[1].trim().toLowerCase();
const grch37Prefix = 'grch37:';
const grch38Prefix = 'grch38:';

if (
(alt1.startsWith(grch37Prefix) && alt2.startsWith(grch38Prefix)) ||
(alt1.startsWith(grch38Prefix) && alt2.startsWith(grch37Prefix))
) {
return true;
}
return false;
}

export function compareMutationsByDeleted(mut1: Mutation, mut2: Mutation) {
const mut1IsDeleted = mut1.name_review?.removed || false;
const mut2IsDeleted = mut2.name_review?.removed || false;
Expand Down