Commit b0380f32 authored by hjulienne's avatar hjulienne
Browse files

add debug print

parent 9c12fe0a
Pipeline #42974 passed with stages
in 1 minute
......@@ -59,7 +59,9 @@ def launch_preprocessing(args):
ref = jp.map_reference.read_reference(args.ref_path, bool(args.mask_MHC), float(args.minimum_MAF), region_to_mask=eval(args.additional_masked_region))
print(ref.shape)
print(ref.head())
print(gw_df.shape)
print(gw_df.head())
mgwas = jp.map_reference.map_on_ref_panel(gw_df, ref, gwas_map.loc[tag, "index_type"])
print(mgwas.shape)
mgwas = jp.map_reference.compute_snp_alignement(mgwas)
......
......@@ -134,7 +134,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
print("Reading file:")
print(gwas_internal_link)
is_gzipped = re.search(r".gz$", gwas_internal_link)
is_gzipped = re.search(r".gz|.bgz$", gwas_internal_link)
if is_gzipped:
compression = 'gzip'
......
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