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ToniWestbrook / paladin

Protein Alignment and Detection Interface
MIT License
60 stars 7 forks source link

paladin align -o #19

Closed macmanes closed 9 years ago

macmanes commented 9 years ago

-o does not seem to be parsed properly. setting it to -o 100 has no effect on number of reads mapped.

ToniWestbrook commented 9 years ago

Sorry - my bad again - the minimum ORF length functionality still isn't active, I just forgot to remove the description from the help file for now. I have an update I'm going to try to release tonight, and I'll incorporate that in for now (more on that later today)

macmanes commented 9 years ago

About release: let's see if we can validate the permissive align settings -B0 -O0 -E0 -L0 with the @Vadavim scoring code and if they look make these the default settings.

ToniWestbrook commented 9 years ago

Description removed for now - the next release this/next week (0.3.0) will bring back minimum ORF length - we can test fully and discuss the results

Louisa-Normington commented 9 years ago

Where is the sam file for -B0 -O0 -E0 -L0 located? Jordan needs to use it for his script.