From 65577bbf062c7a711c90ce1257c773164e249b97 Mon Sep 17 00:00:00 2001
From: Daniel Richter <56433682+darichter87@users.noreply.github.com>
Date: Mon, 15 May 2023 14:18:15 +0200
Subject: [PATCH] Update fqfilter_v2.pl

Fix whitespace Problem in read-IDs.
For read-IDs containing multiple whitespaces, only the last part was removed due to greedy matching of only one whitespace.
Subsequently, read-IDs within the *.unmapped.bam can contain whitespaces, which cause problems when mapping with STAR (all reads will consist of one single 'N' nucleotide).
Adapting the pattern to just match the first non-whitespace character-set within the read-ID fixes this Problem.
---
 fqfilter_v2.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/fqfilter_v2.pl b/fqfilter_v2.pl
index 0e88a8a..b200161 100644
--- a/fqfilter_v2.pl
+++ b/fqfilter_v2.pl
@@ -305,11 +305,11 @@ BEGIN
       chomp($rid);
 
       if($rid =~ m/^\@.*\s/){
-        $rid =~ m/^\@(.*)\s/;
+        $rid =~ m/^\@(\S+)/;
         $ridtmp = $1;
       }
       else{
-        $rid =~ m/^\@(.*)/;
+        $rid =~ m/^\@(\S+)/;
         $ridtmp = $1;
       }