From 77e1cba32a3ad869b76b13844e5b35c70667f469 Mon Sep 17 00:00:00 2001 From: Jakob Nybo Nissen Date: Tue, 10 Dec 2024 17:08:44 +0100 Subject: [PATCH] Use the correct binsplitter in TaxVamb (#377) Previously, TaxVamb incorrectly used the inert splitter instead of the one specified on command-line, when loading its composition. Since the binsplitter is properly initialized in `calc_tnf`, such that it will not attempt to binsplit on 'C' if this separator is not present, the use of an inert splitter skipped this initialization. This caused a bug where the lack of a separator was not detected until the data was clustered, far too late. --- vamb/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vamb/__main__.py b/vamb/__main__.py index d3a6c94b..d8fe9226 100755 --- a/vamb/__main__.py +++ b/vamb/__main__.py @@ -1509,7 +1509,7 @@ def run_vaevae(opt: BinTaxVambOptions): vamb_options=opt.common.general, comp_options=opt.common.comp, abundance_options=opt.common.abundance, - binsplitter=vamb.vambtools.BinSplitter.inert_splitter(), + binsplitter=opt.common.output.binsplitter, ) abundance, tnfs, lengths, contignames = ( abundance.matrix,