This PR implements the import of STAR-Fusion+FusionInspector output in order to get a plotFusionReads-like plot. FusionInspector creates a virtual 'mini genome' to which the fusion reads are again aligned. Unfortunately, the chromosomes and coordinates are therefore completely different, so plotFusionReads needs some simplifications (function plotFusionReadsSimple) to work, and plotCircle, plotFusions and plotTranscripts all fail, because of the different coordinate systems.
It may still be useful to some people. E.g., I currently read the fusion data in in two ways: plain STAR-Fusion for plotCircle, plotFusions and plotTranscripts; and in useFusionInspector=TRUE mode for plotFusionReadsSimple. (The latter is still really bare bones BTW)
This PR implements the import of STAR-Fusion+FusionInspector output in order to get a
plotFusionReads-like plot. FusionInspector creates a virtual 'mini genome' to which the fusion reads are again aligned. Unfortunately, the chromosomes and coordinates are therefore completely different, soplotFusionReadsneeds some simplifications (functionplotFusionReadsSimple) to work, andplotCircle,plotFusionsandplotTranscriptsall fail, because of the different coordinate systems.It may still be useful to some people. E.g., I currently read the fusion data in in two ways: plain STAR-Fusion for
plotCircle,plotFusionsandplotTranscripts; and inuseFusionInspector=TRUEmode forplotFusionReadsSimple. (The latter is still really bare bones BTW)