Filtering doesn't seem to do anything

[KatyMunson]

The -f parameter doesn't seem to do anything.

(base) kmiyamot@liger$ rdeval --version
rdeval v0.0.5
Giulio Formenti giulio.formenti@gmail.com
(base) kmiyamot@liger$ rdeval myONT.rd
+++Read summary+++:
# reads: 17267657
Total read length: 119916190443
Average read length: 6944.55
Read N50: 32409
Smallest read length: 1
Largest read length: 1731095
Coverage: inf
GC content %: 40.43
Base composition (A:C:T:G): 35654976733:24053725773:35779931816:24427556121
Average per base quality: 18.38
(base) kmiyamot@liger$ rdeval myONT.rd --filter 'q>20 & l>10'
+++Read summary+++:
# reads: 17267657
Total read length: 119916190443
Average read length: 6944.55
Read N50: 32409
Smallest read length: 1
Largest read length: 1731095
Coverage: inf
GC content %: 40.43
Base composition (A:C:T:G): 35654976733:24053725773:35779931816:24427556121
Average per base quality: 18.38

[gf777]

Hi @KatyMunson again many thanks for the useful feedback!
Good catch, so on .rd files specifically this combination doesn't filter. You can filter the per-read output of .rd files as in e.g. rdeval myONT.rd --filter 'q>20 & l>10' -qa
We will fix it with the next release. Cheers

[KatyMunson]

Thanks Guilio! Would love to see output files also reflect any filtering done (e.g. rdeval myONT.rd --filter 'q>20 & l>10' -o filtered.rd)

[gf777]

Hello @KatyMunson,
Again thanks for flagging this. We have now added this to both filter the report and to output to a new .rd file. We cannot update the ACGT content as that would require major refactoring, so if the filter is effective at removing some reads we zero ACGT counts out for now. It would make sense for this to be part of rdeval 2.0 (note for self). Have a look, and if you are happy I'll close the issue, thanks!