search

SACGF / cdot

Transcript versions for HGVS libraries
MIT License
29 stars 5 forks source link

Implement get_alignments_for_region #47

Closed davmlaw closed 1 year ago

davmlaw commented 1 year ago

This is only ever used by get_tx_for_region, which I implemented by itself

UTA implements get_tx_for_region by calling get_alignments_for_region we could do the same

ccaitlingo commented 1 year ago

You're right, probably no need to implement get_alignments_for_region.

However, if you wanted to, you could consider raising an error in get_tx_for_region if an align method other that splign is used, instead of returning an empty list as it currently does.

I don't know how often hgvs users switch to using blat/others instead of splign. You might be in the clear for the most part since the default method is set to splign in hgvs's defaults.ini (just as the reference genome is set to GRCh38).

davmlaw commented 1 year ago

Implemented get_alignments_for_region via get_tx_for_region as it was super easy to do, added comment that you should probably use get_tx_for_region instead. Will remove if we decide to remove from interface Throw exception if alt_aln_method is ever not 'splign'