--allow-outies by default ON

[Arkadiy-Garber]

Hi!

I've been running flash2 that I installed via conda. There does not appear to be a way to turn off the --allow-outies option. Flash2 combines both in innie and outie orientations with and without this flag.

Thanks!
Arkadiy

[msettles]

well depends on what you mean by innie/outie, its different from the original implementation of FLASH (where outies are reads from the mate-pair protocol) "our" outies are paired-end reads that produce complete overlaps, where the overhangs are adapter sequence and get trimmed off. So why would you want to turn that option off? WE may have hardcoded it on, and leave the param to maintain backwards compatibility. I don't recall. We've also moved on from Flash2 in favor of our new project HTStream https://github.com/s4hts/HTStream, which has hts_Overlapper