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get_coverage_filter: blast filter cutoff #8

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luca-Wang opened this issue Jan 12, 2021 · 1 comment

luca-Wang commented Jan 12, 2021

Hi，

I am puzzling about which cutoff to use in blast filter step:
if ($coverage < 0.8 or $arr[2] < 90)
or
if ($coverage < 0.8 and $arr[2] < 90)

why you final use the "and" ?

thanks in advance !

Owner

Zhuxitong commented Jun 6, 2021

@luca-Wang Sorry for the very late reply. I am busy with some other projects. Now I have some time to update ppsPCP.

We use and to ensue high confidence of PAVs and we assume the pan-genome is built with colse related species.

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