Commit d378743c authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

fixed realigned window

parent eb9d89e8
......@@ -31,10 +31,11 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
If not, the coded and other allele are inverted and the zscore sign
is inverted also.
allele_inverted = (ref_panel.loc[zscore.index, 'Ref_all'] != zscore.A0)
sub_ref_panel = ref_panel.loc[zscore.index]
allele_inverted = (sub_ref_panel['Ref_all'] != zscore.A0)
zscore.loc[allele_inverted, "A0"] = ref_panel.alt_all
zscore.loc[allele_inverted, "A1"] = ref_panel.Ref_all
zscore.loc[allele_inverted, "A0"] = sub_ref_panel.loc[allele_inverted].Ref_all
zscore.loc[allele_inverted, "A1"] = sub_ref_panel.loc[allele_inverted].alt_all
zscore.loc[allele_inverted, "Z"] = - zscore.loc[allele_inverted, "Z"]
return zscore
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