# HG changeset patch
# User clifinder
# Date 1581717804 18000
# Node ID 3e33703874415b012d4bbddd4e3577253f2fc441
# Parent  40695c10cfbd43d219703b088365e7137e2ff61d
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 94d5cab008ee4422a8ba63468532d3bb552abcd5"

diff -r 40695c10cfbd -r 3e3370387441 script/CLIFinder.pl
--- a/script/CLIFinder.pl	Thu Feb 13 08:37:34 2020 -0500
+++ b/script/CLIFinder.pl	Fri Feb 14 17:03:24 2020 -0500
@@ -528,12 +528,11 @@
     
     ##looking for flag of the alignment and keep only good reads##
     ##Find if it aligns on R1 or on R2##
-    
-    if ($line[1] == 73 || $line[1] == 89 || $line[1] == 117 || $line[1] == 69 || $line[1] == 133 || $line[1] == 181 || $line[1] == 153|| $line[1] == 137)
+    unless($line[1] & 2 || ($line[1] & 4 && $line[1] & 8))
     {
       if ( $Bdir == 0
-              || ($Bdir == 1 && (($line[1] & 064 && $line[1] & 8) || ($line[1] & 128 && $line[1] & 4)))
-              || ($Bdir == 2 && (($line[1] & 128 && $line[1] & 8) || ($line[1] & 064 && $line[1] & 4))) )
+              || ($Bdir == 1 && (($line[1] & 64 && $line[1] & 8) || ($line[1] & 128 && $line[1] & 4)))
+              || ($Bdir == 2 && (($line[1] & 128 && $line[1] & 8) || ($line[1] & 64 && $line[1] & 4))) )
       {
         $cmp++;
         $sequence = $line[9];