replace vcf with ref_fasta when reading reference genome

atgu · Jan 31, 2025 · d13b411 · d13b411
1 parent 56163d8
commit d13b411
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/gwaspy/check_alleles/check_alleles.py b/gwaspy/check_alleles/check_alleles.py
@@ -95,8 +95,8 @@ def fix_alleles(
 
         return j
 
-    ref_fasta_in = batch.read_input_group(**{'vcf': reference_path,
-                                        'index': f'{reference_path}.fai'})
+    ref_fasta_in = batch.read_input_group(**{'ref_fasta': reference_path,
+                                             'ref_fasta_index': f'{reference_path}.fai'})
     ref_size = round(size(reference_path))
 
     if "CNUMBER" in input_path:  # input VCF is already split by chromosome