Reading fusion seq #23
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... 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 ... (cherry picked from commit a8fc9cb)
untested, and only when you calculated it using the FusionAnnotator
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Note that this PR is deliberately against a much older commit (close to stainlagstad's master), as it is independent of my recent FusionInspector PR's |
stianlagstad
requested changes
Mar 4, 2018
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Closing in favor of #56. Thank you @plijnzaad ! |
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STAR-fusion >= 1.2.0, when run with
--denovo_reconstructhas a columnFUSION_CDSin output filestar-fusion.fusion_predictions.abridged.annotated.coding_effect.tsvwhich contains the fusion sequence. This PR extracts it and adds it to the fusion object (in addition to setting attributeinframead also addingFFPMandannotstofusionToolSpecificData)