Is your feature request related to a problem? Please describe.
Principle of each app should do one thing and one thing well, is violated with this optoins
Describe the solution you'd like
remove the option and functionality from hts_SuperDeduper for
-a [ --inform-avg-qual-score ] arg (=5)
Avg quality score to consider a read
informative (min 1, max 10000)
This functionality is a hold over from our flash2 implementation to remove likely primer dimers. These reads should be removed using other utilities like QWindowTrim and LengthFilter
Is your feature request related to a problem? Please describe. Principle of each app should do one thing and one thing well, is violated with this optoins
Describe the solution you'd like remove the option and functionality from hts_SuperDeduper for -a [ --inform-avg-qual-score ] arg (=5) Avg quality score to consider a read informative (min 1, max 10000) This functionality is a hold over from our flash2 implementation to remove likely primer dimers. These reads should be removed using other utilities like QWindowTrim and LengthFilter
Describe alternatives you've considered N/A
Additional context N/A