From 28df0c35c164f79cf21f8c1f0e527f715015966f Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 25 May 2025 19:38:01 +0200
Subject: [PATCH] correction of the IR detection

---
 detectors/cds/bin/go_cds.sh         | 2 +-
 detectors/normalize/lib/selectIR.py | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/detectors/cds/bin/go_cds.sh b/detectors/cds/bin/go_cds.sh
index b89f244..6891de8 100755
--- a/detectors/cds/bin/go_cds.sh
+++ b/detectors/cds/bin/go_cds.sh
@@ -111,7 +111,7 @@ if [[ "$cdsdetection_pass3" == "yes" ]] ; then
         loginfo $fams
         loginfo "running pass3:$dir exonerate of $Genome on $DbRoot"
         for f in $fams ; do
-          tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
+          echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
         done
     fi
     done) | parallel -j $Threads
diff --git a/detectors/normalize/lib/selectIR.py b/detectors/normalize/lib/selectIR.py
index 9574e33..c69a9ee 100755
--- a/detectors/normalize/lib/selectIR.py
+++ b/detectors/normalize/lib/selectIR.py
@@ -120,8 +120,7 @@ for line in repeats:
     # pvalue= 
     # print("c.lsc = %f c.ssc = %f   o.lsc = %f o.ssc = %f score = %6.4f (len=%d)" % (c_lsc,c_ssc,o_lsc,o_ssc,score,len1),
     #      file=sys.stderr)
-        
-    if (score >= scoreMax) and ((len1 > len1Max) or (len2 > len2Max)):
+    if (int(score*100) >= int(scoreMax*100)) and ((len1 > len1Max) or (len2 > len2Max)):
         scoreMax = score
         pos1Max  = pos1
         pos2Max  = pos2