Hello, guys in forum.
I have a question which is about filtering reads in “sam” input.
As you see in the below picture:
(search “input_type == ‘sam’” in metaphlan 3.0.9 code and you will find it.)
And I sincerely wanna know the reason for retaining reads of which the marker starts with “GeneID:”.
Thanks a lot !
Hi @cquxiaoy
That part of the code is to always keep the hits against the viral markers in MetaPhlAn 2 and 3