From 2223f50c6482349d2cdcf072bef9d2a715f150aa Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 2 Dec 2024 11:10:27 +0000
Subject: [PATCH] remove temp file produced

---
 tbprofiler/consensus.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tbprofiler/consensus.py b/tbprofiler/consensus.py
index d82fa09..2bc8fc1 100644
--- a/tbprofiler/consensus.py
+++ b/tbprofiler/consensus.py
@@ -71,6 +71,7 @@ def get_consensus_vcf(sample: str,input_vcf: str,args: argparse.Namespace) -> st
     run_cmd(f"cat {args.conf['ref']} {consensus_file}> {tmp_aln}")
     outfile = f"{args.files_prefix}.masked.vcf"
     run_cmd(f"fa2vcf.py {tmp_aln} {outfile}")
-    os.remove(tmp_aln)
+    run_cmd(f'rm {tmp_aln} {tmp_aln}.fai')
+    
     return outfile