featureCounts setting paired flag when it shouldn't

[serine]

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.