From 621efa9410a27d660b0baf8c0cf1a744328096bd Mon Sep 17 00:00:00 2001
From: Amine Ghozlane <amine.ghozlane@pasteur.fr>
Date: Mon, 18 Nov 2024 15:18:18 +0100
Subject: [PATCH] Move vcf with shutil instead of rename

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

diff --git a/meteor/variantcalling.py b/meteor/variantcalling.py
index 484143f..4db4179 100644
--- a/meteor/variantcalling.py
+++ b/meteor/variantcalling.py
@@ -17,6 +17,7 @@
 import lzma
 import bgzip
 import pickle
+import shutil
 from subprocess import CalledProcessError, run, Popen, PIPE
 from dataclasses import dataclass
 from pathlib import Path
@@ -31,7 +32,6 @@
 import pandas as pd
 from typing import ClassVar
 import numpy as np
-import pysam
 
 
 def run_freebayes_chunk(
@@ -666,7 +666,7 @@ def execute(self) -> None:
                 logging.info("Merging vcf")
                 self.merge_vcf_files(vcf_chunk_files, vcf_file)
             else:
-                Path(vcf_chunk_files[0]).rename(vcf_file)
+                shutil.move(str(vcf_chunk_files[0]), str(vcf_file.resolve()))
         logging.info(
             "Completed freebayes step in %f seconds", perf_counter() - startfreebayes
         )