diff --git a/jass_preprocessing/map_reference.py b/jass_preprocessing/map_reference.py index 65550fd224e1d2ceb5a0c04c1547cf7e9119fea3..260e16e9d4939bc6d678f37e8e7903aa8fbeb324 100644 --- a/jass_preprocessing/map_reference.py +++ b/jass_preprocessing/map_reference.py @@ -21,8 +21,10 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio """ ref = pd.read_csv(gwas_reference_panel, header=None, sep= "\t", names =[ 'chr', "snp_id", "MAF","pos", "ref", "alt"], - dtype = {"chr": str, "snp_id":str, "MAF": np.double, "pos":np.int64, "ref":str, "alt":str}, + dtype = {"chr": str, "snp_id":str, "MAF": np.double, "pos":np.double, "ref":str, "alt":str}, index_col="snp_id") + ref = ref.loc[~ref.pos.isnull()] + ref.pos = ref.pos.astype('int') def sorted_alleles(x): return "".join(sorted(x))