From 6efa67c1171597c5dc65f586276c8eded25e2316 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 27 Feb 2025 13:49:31 +0100
Subject: [PATCH] #45 fix variable names

---
 viloca/shorah_snv.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/viloca/shorah_snv.py b/viloca/shorah_snv.py
index 387273a..efaf113 100644
--- a/viloca/shorah_snv.py
+++ b/viloca/shorah_snv.py
@@ -555,8 +555,8 @@ def main(args):
             _, chrom, beg, end, _ = line.rstrip().split("\t")
 
             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")
+            haplo_filename = os.path.join(working_dir, file_stem + ".reads-support.fas")
+            ref_name = os.path.join(working_dir, file_stem + ".ref.fas")
             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"