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funannotate sort --minlen not working #896

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abretaud opened this issue Apr 6, 2023 · 2 comments
Closed

funannotate sort --minlen not working #896

abretaud opened this issue Apr 6, 2023 · 2 comments

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@abretaud
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abretaud commented Apr 6, 2023

Are you using the latest release?
using master branch

Describe the bug
the --minlen option of funannotate sort isno longer working (writing smaller contigs)

What command did you issue?
funannotate sort --input input.fa --out output.fa --base 'something' --minlen 2100

The if/else logic is not working as expected after recent refactoring at

if minlen and length >= int(minlen):

@hyphaltip
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I can fix that - you can also use AAFTF for sorting.

nextgenusfs pushed a commit that referenced this issue Apr 11, 2023
@abretaud
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Thanks, the fix works!

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