From 01a14bdab9075460645523ad3d2ffda0ece97e25 Mon Sep 17 00:00:00 2001
From: kevm29 <46615988+kevm29@users.noreply.github.com>
Date: Thu, 28 Jan 2021 14:46:13 +0100
Subject: [PATCH] Update split_reads.py
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Ajout de l'option -fc pour forcer le gunzippage d'un fichier lié par un lien symbolique, sinon il y a un blocage "Too many levels of symbolic links"
---
 bin/utils/split_reads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/utils/split_reads.py b/bin/utils/split_reads.py
index d8a22fc..d93ed17 100755
--- a/bin/utils/split_reads.py
+++ b/bin/utils/split_reads.py
@@ -25,7 +25,7 @@
 
 if filename.endswith('.gz'):
     prefix = re.sub('((.fastq)|(.fq)).gz','_part', os.path.join(out, os.path.basename(filename)))
-    cmd = "zcat {} | split -l {} -d - {}".format(
+    cmd = "zcat -fc {} | split -l {} -d - {}".format(
         filename, nlines, prefix)
 else:
     prefix = re.sub('(.fastq)|(.fq)','_part', os.path.join(out, os.path.basename(filename)))