feature request: handle paired interleaved reads

[rosekantor]

Hi Mike,

Any chance you'd be willing to handle paired interleaved reads in the next update? The main issue is with the sam filtering flags. Right now, "paired" requires 2 read files input and filtering handles paired reads, while "unpaired" is the only option if you have a single reads file. But the sam filter will treat then as unpaired.

Relevant code starts around:

EsViritu/src/EsViritu/esv_funcs.py

Line 158 in 539f522

if paired == "paired":

(although I know there's also relevant parts in the fastp stats as well).

Thanks for considering,
Rose

[mtisza1]

Hey @rosekantor, thanks for opening the issue. I think it is time to properly support interleaved FASTQs!

Release v1.3.3 implements the feature (see #46). It works well based on my testing, but let me know if anything is off.

Best,

Mike