expect liftover chain files to be in same path ...

as the liftover config
kriese · Jun 3, 2022 · 3ff99f8 · 3ff99f8
1 parent b71d483
commit 3ff99f8
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/workflow/scripts/ref_cut.py b/workflow/scripts/ref_cut.py
@@ -57,10 +57,11 @@ def collect_liftover(args):
         "t2tv2": ["chain_hg38_to_t2tv1", "chain_t2tv1_to_t2tv2"]
     """
     liftover_jumps = json.load(open(args.liftover_paths, "r"))
+    liftover_root = args.liftover_paths.parent
     for chain_file_route in liftover_jumps.values():
         for chain_file in chain_file_route:
             if not chain_file in liftover_chain_files:
-                liftover_chain_files[chain_file] = LiftOver(str(chain_file))
+                liftover_chain_files[chain_file] = LiftOver(str(liftover_root / chain_file))
 
     alt_regions = []
     for ref_idx, (alt_ref_name, alt_ref) in enumerate(zip(alt_ref_names, alt_references)):