I'd like to propose additional options for paired-end trimming that will enable different quality and length thresholds to be used to decide whether to keep a single read if one but not both mates fail the paired-end quality filters. I will implement this and submit a pull request. The options will look like this:
-L, --orphan-length-threshold, length threshold to use for retaining a single mate if one (but not both) mate fails the paired-end length threshold. Defaults to the value specified for --length-threshold.
-Q --orphan-qual-threshold, quality threshold to use for retaining a single mate if one (but not both) mate fails the paired-end quality threshold. Defaults to the value specified for --qual-threshold.
I'd like to propose additional options for paired-end trimming that will enable different quality and length thresholds to be used to decide whether to keep a single read if one but not both mates fail the paired-end quality filters. I will implement this and submit a pull request. The options will look like this:
-L, --orphan-length-threshold, length threshold to use for retaining a single mate if one (but not both) mate fails the paired-end length threshold. Defaults to the value specified for --length-threshold. -Q --orphan-qual-threshold, quality threshold to use for retaining a single mate if one (but not both) mate fails the paired-end quality threshold. Defaults to the value specified for --qual-threshold.