From 4c4e5ab7ca1266df8d22e0416cb9d18035181749 Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.fr>
Date: Sun, 7 Jan 2024 15:53:07 +0100
Subject: [PATCH] fix bug mergeflagstats
---
frangiPANe/snakefiles/merge_flagstat.smk | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/frangiPANe/snakefiles/merge_flagstat.smk b/frangiPANe/snakefiles/merge_flagstat.smk
index 8c4d82e..c671745 100644
--- a/frangiPANe/snakefiles/merge_flagstat.smk
+++ b/frangiPANe/snakefiles/merge_flagstat.smk
@@ -34,7 +34,7 @@ rule merge_flagstat:
for line in stat:
line = line.rstrip()
- if 'mapped (' in line or ('paired (' in line and not 'primary' in line) or 'singleton' in line:
+ if ('mapped (' in line and not 'primary' in line) or 'paired (' in line or 'singleton' in line:
# print(line.split('(')[1].split('%')[0])
newLine += f",{line.split('(')[1].split('%')[0]}"
--
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