Import fusion inspector support#21
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plijnzaad wants to merge 12 commits into
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leave this up to end user (e.g. MT-chr3 fusions display fine)
(cherry picked from commit f17c89decb83c2bc97811231b97f546672767d03)
(cherry picked from commit 8768ce180b2c7b324c980940e4457f7be0fa6835)
... but only if column PROT_FUSION_TYPE is available (i.e. when reading star-fusion.fusion_predictions.abridged.annotated.coding_effect.tsv ) If the (default) "star-fusion.fusion_predictions.abridged.tsv" file is used, inframe remains NA (and a warning is issued) now also setting fusion@inframe ...
... to make R CMD check shut up
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I had hoped that Chimeraviz could also do a
plotFusionReadstype 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