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config parameterization of GATHER_MIN_MATCHES #211

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taylorreiter opened this issue Mar 9, 2022 · 0 comments
Open

config parameterization of GATHER_MIN_MATCHES #211

taylorreiter opened this issue Mar 9, 2022 · 0 comments
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enhancement New feature or request

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@taylorreiter
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charcoal/charcoal/compare_taxonomy.py

Line 23 in b9c2b8d

GATHER_MIN_MATCHES=3

GATHER_MIN_MATCHES is hardcoded to 3, which I think is great in the context of MAG/genome decontamination, but I just went to use charcoal to sort assembled contigs of one lineage away from all of the others, and in this particular case they're all very short contigs, but I would love to throw away the ones that I have high suspicions are not my lineage, even if that means dropping the threshold to 1. Any way, this is all to say, i have dreamed up a usecase where it would be great to be able to control GATHER_MIN_MATCHES
@taylorreiter taylorreiter added the enhancement New feature or request label Mar 9, 2022
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