Brendan O'Donnell

Fix ins or dups where splice region is preserved

10

Fixes #714. Fixes ins or dup variants spanning the intron/exon or exon/intron boundary where the splice site & region remain completely intact.

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

15

Fixes #655 Certain ins or dup variants that occur at the intron/exon boundaries have non-zero offsets but are still coding. This PR ensures that projections return accurate var_p representations for...

c_to_p for dups that start in transcript but end in UTR

3

Any duplications with an end position at or past the stop codon should be classified as 3'UTR regardless of start position. Currently mapping `NM_153223.3:c.2959_*1dup` yields `NP_694955.2:p.(Met1?)`. We believe that should...

c_to_p at intron/exon boundary where splice region is preserved

3

We have a number of ins or dup variants at the intron/exon or exon/intron boundary that return no protein change that we believe should be treated as coding because the...

Add variant region condition for dups ending in UTR

1

Fixes #715. Classify `ins` or `dup` variants as 3'UTR if the end position is in the UTR region regardless of the start position.

Check ints for the end of string before seperator

1

If an integer matcher is the final element of a Trie it interprets the null at the end of the string as a separator character and pushes it back onto...

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

5

Fixes #655 This PR is offered as an alternative to https://github.com/biocommons/hgvs/pull/709. It solves the same problem, that certain ins or dup variants that occur at the intron/exon boundaries have non-zero...