gostachowiak comments

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                                            gostachowiak

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

@reece reminder about this PR. If it would be easier to have a meeting to review together, we would be happy to do that. We will need to consider forking...

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

@reece Thank you for your comments and questions. It helped us to identify a few issues and clarify our thinking. After making a few tweaks to the pull request, here...

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

@reece Yes, I think you understand correctly-- the result depends on the intronic sequence. 1. I think the first step is to see if there's agreement on the problem we're...

Fix ins or dups where splice region is preserved

High-level explanation of this pull request: - HGVS nomenclature has the 3' shifting rule. so all cdots and pdots are shifted to the right - However, 3' shifting is arbitrary...

Fix ins or dups where splice region is preserved

I also wanted to mention that we discovered this because some fraction of FLT3 ITDs currently get missed when using the hgvs package (including one added to the unit tests)....