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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Import fusion inspector support #21

Open plijnzaad opened 6 years ago

plijnzaad commented 6 years ago

I had hoped that Chimeraviz could also do a plotFusionReads type plot with output from STAR-Fusion+FusionInspector, but that is unfortunately not the case, the data is too different.

It turns out that FusionInspector (part of the STAR-Fusion suite) produces most of the things needed to do a fusion reads plot, by creating a virtual 'mini genome' to which the fusion reads are again aligned.

I therefore wrote an extension that can deal with this. This pull request sets the stage for making that possible: it makes a few (star-fusion output-specific) things slightly more general. If all is well, things should remain working as before.

I will issue another PR later on with code that implements the importing of FusionInspector results

plijnzaad commented 6 years ago

Note: this PR also includes those implemented by PR #18, #19 and #20 . I think they are largely independent, so you prolly can cherrypick your way around

stianlagstad commented 6 years ago

Thank you very much! :) I'll wait with this one until we've merged #18, #19 and #20.