Dave Lawrence
Dave Lawrence
There is often the need for picking 1 transcript for a gene. This is often referred to as the canonical transcript, and nowadays (clinically) is usually the [MANE](https://www.ncbi.nlm.nih.gov/refseq/MANE/) transcript It...
Could you please remove the chrM contig header lines from the GRCh37 sites file? (and may as well remove the other unused ones) I found this as I use the...
raw_header is modified - loading a VCF with bad contigs in header, it has fake contigs with no length added to it. This always happens on 1 machine, not on...
I understand a variant growing bigger if the destination reference has an insertion, but shouldn't it be put back when it goes the other way? ``` original_hgvs = "NM_015120.4(ALMS1):c.36_38dupGGA" def...
Converting back and forth fails in this case due to being normalized off the transcript ``` In [1]: var_n = parse("NR_003051.3:n.1_2insAGGACGTG") In [2]: var_g = n_to_g(var_n) In [3]: var_g Out[3]:...
Thanks for the tool! I know about the warning: > Warning: input VCF includes symbolic alleles that might not properly lift over but thought it would be useful to explicitly...
Raised in hackathon discussion of uncertainties pull request (one of the main points of this issue is to be able to get that pull request through as is, and handle...
There is now a pre-commit to run ruff-format But the source code isn't currently formatted This means if you work on a file, it'll be auto-formatted and so any formatting...
Raised new issue so as not to derail the pull request going through. In a few places, there is implicit behavior (such as taking inner interval) - we should allow...
Looking in the parser syntax (hgvs.pymeta) most of the uncertainty is only applied for g. ie ```uncertain_g_interval``` - hopefully we just need to copy it for c. but here's what's...