check if input index file exists

atgu · Feb 14, 2024 · 6329cc1 · 6329cc1
1 parent d4507bd
commit 6329cc1
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/gwaspy/phasing/shapeit5_phase.py b/gwaspy/phasing/shapeit5_phase.py
@@ -229,6 +229,9 @@ def concatenate_rare_chunks(
             chrom_vcf = batch.read_input_group(**{'vcf': input_path,
                                                   'index': input_idx})
 
+        if not hfs.exists(input_idx):
+            raise SystemExit('GWASpy requires the input file to be indexed (.tbi or .csi). Found none, exiting')
+
         vcf_size = round(size(vcf_path))
 
         if reference_path: