Closed jaclyn-taroni closed 3 years ago
Because I'm not merging into master
, no review required. Feel free to merge if this looks good, @cbethell !
Because I'm not merging into
master
, no review required. Feel free to merge if this looks good, @cbethell !
Took a careful look at things locally and everything looks good ✅ so I'll go ahead and merge (then address and re-run things over on #1009)
Related to #1009 - We were having an issue where reciprocal fusions were showing up inappropriately as multi-hit fusions in the OncoPrints. During review, using
reciprocal_exists
in the putative oncogenic fusion file was raised https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1009#pullrequestreview-647703181 which I came across during my own review of #1009. It occurred to me that we only need to sort gene partners of fusions in alphabetical orders when we know a reciprocal fusion exists, where we then use the sorted results to collapse reciprocal fusions/make sure we're only counting them once.So here I'm proposing fusion code updates that do the following:
reciprocal_exists == TRUE
andreciprocal_exists == FALSE
separately, based on the considerations for each (e.g., sorting forreciprocal_exists == TRUE
only) - I draw from the sorting code in #1009 but usestringr
functionality because personal preference, mostlymaster
@cbethell I spot checked a couple differences between this code and what's in #1009 and it looks like this code correctly IDs some multi-hit fusions missed in #1009.