Fix main function arguments

workflow/scripts/weighted_distances.py

@@ -107,11 +107,10 @@ def build_cache(df: pd.DataFrame, reference: Seq):
     return cache
 
 
-def buildm(df: pd.DataFrame, sample_names: list, cache: dict) -> pd.DataFrame:
+def buildm(positions: List[int], sample_names: list, cache: dict) -> pd.DataFrame:
     # Compute matrix
     logging.debug(f"Filling distance matrix")
     nsamples = len(sample_names)
-    positions = df["POS"].astype("Int64").unique().tolist()
     m = np.zeros((nsamples, nsamples), np.float64)
     for i, sample1 in enumerate(sample_names):
         for j, sample2 in enumerate(sample_names):
@@ -140,10 +139,11 @@ def main():
 
     # Pre-compute one-sample measurements
     logging.info(f"Caching computations")
-    cache = build_cache(df, ancestor.seq)
+    cache = build_cache(variant_table, ancestor.seq)
 
     logging.info(f"Calculating matrix")
-    df = buildm(variant_table, sample_names, cache)
+    positions = variant_table["POS"].astype("Int64").unique().tolist()
+    df = buildm(positions, sample_names, cache)
 
     logging.info("Writing results")
     df.to_csv(snakemake.output.distances)