Feature Requests for v3.8

[ahanden]

This is an ongoing list of feature requests for REDItools. The goal is to have them all included in the v3.8 release.

• Let REDItools resume from partially finished jobs. (PR Resume #107)
• Determine maximum number of threads (96 appears to be too many) (PR Added check maximum open file check for thread count. #111)
• Option to use old Strand column value ("-"=0, "+"=1, "*"=2) (PR Strand symbols #110)
• Include the strand column from BED files for filtering analysis output
• Allow DNA and RNA to be analyzed simultaneously by analyze without needing to use annotate

Not being implemented

• Change temporary filenames to match chromosome/region being analyzed instead of gibberish.

[ahanden]

The temporary filename thing is not going to be addressed. It turns out that you can name your chromosomes with all kinds of special characters that are simply beyond what we can control for programmatically. Rather than try to sanitize filenames, I am considering the region file list from #107 to be sufficient.