From 941060e07293adc6c5b10042b1b84b2e8c446a03 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 27 Feb 2025 13:24:56 +0100
Subject: [PATCH] #45 fix variable names

---
 viloca/shorah_snv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/viloca/shorah_snv.py b/viloca/shorah_snv.py
index 34c44b2..387273a 100644
--- a/viloca/shorah_snv.py
+++ b/viloca/shorah_snv.py
@@ -557,7 +557,7 @@ def main(args):
             file_stem = "w-%s-%s-%s" % (chrom, beg, end)
             haplo_filename = os.path.join(working_dir, "haplotypes", file_stem + ".reads-support.fas")
             ref_name = os.path.join(working_dir, "haplotypes", file_stem + ".ref.fas")
-            tmp_df.append(get_cooccuring_muts_haplo_df(fname_haplo, fname_ref, beg,end,chrom))
+            tmp_df.append(get_cooccuring_muts_haplo_df(haplo_filename, ref_name, beg,end,chrom))
     pd.concat(tmp_df).to_csv("cooccurring_mutations.csv")
     # finish  write: "cooccurring_mutations.csv"