From 043ef7dc63adf172745fa7db2cc0e07f8c1d9a2e Mon Sep 17 00:00:00 2001
From: Diego Fuentes Palacios <43205584+Dfupa@users.noreply.github.com>
Date: Tue, 12 Dec 2023 11:56:13 +0100
Subject: [PATCH] Account for uncompressed fq in filterReads.py

---
 bin/filterReads.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/bin/filterReads.py b/bin/filterReads.py
index c11edd4..4ae997e 100755
--- a/bin/filterReads.py
+++ b/bin/filterReads.py
@@ -143,10 +143,15 @@ def rawtrimmer(infile, minlen, maxlen, limit, minqual, qual64offset, qseq, strip
             continue
         name, seq, quals = read
 
-        #Reformat to string instead of byte
-        name = name.decode('utf-8')
-        seq = seq.decode('utf-8')
-        quals = quals.decode('utf-8')
+        #Reformat to string instead of byte. Add exception in case it is fq instead of fq.gz
+        try:
+            name = name.decode('utf-8')
+            seq = seq.decode('utf-8')
+            quals = quals.decode('utf-8')
+        except:
+            name = name
+            seq = seq
+            quals = quals
         
 
         ## Clip seq & quals @ N ( unknown base )