Brendan O'Donnell

Results 20 comments of Brendan O'Donnell

Fix variant region for ins and dup on intron-exon boundary

Hey @reece, my testing all checked out fine with the latest changes. Thanks again for your feedback.

Fix variant region for ins and dup on intron-exon boundary

Also, this might be semantics but we're not using an arbitrary assembly in the sense that we're picking GRCh37 or GRCh38 randomly. Rather, we're using the assembly tied to the...

Fix variant region for ins and dup on intron-exon boundary

Rebased on main

Fix variant region for ins and dup on intron-exon boundary

Rebased on main

Fix ins or dups where splice region is preserved

We found some examples of duplications where the original logic here didn't shift the variant far enough to to get the expected result. It turned out that for these variants...

Fix ins or dups where splice region is preserved

@reece or @ahwagner can you remove the stale label here? We would still like to get this merged is possible. Thanks!

Fix ins or dups where splice region is preserved

We found a case where trying to map the shifted variant causes an `HGVSInvalidVariantError`. I've added logic to handle this and a test case. The variant is `NM_182758.2:c.2953-31_2953-26dup`. As part...

Fix ins or dups where splice region is preserved

Also rebased on main

Fix ins or dups where splice region is preserved

Rebased on main

c_to_p at intron/exon boundary where splice region is preserved

I am working on a fix for this. I expect to have it ready to submit a PR shortly after PR #709 is merged.