MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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featureCounts setting paired flag when it shouldn't #54

Open serine opened 4 years ago

serine commented 4 years ago

This line of code is buggy. extraOpts is turned into a string by getExtrOpts() function and when extraOpts.index("-p") gets called anything in the path variable will trigger paired become true, which is a bug. I think the right way is to fix getExtrOpts() function and perhaps to rethink how I define and pass extra opts in general.