From 1fadb02077baab133660671888efcdb982dd91b9 Mon Sep 17 00:00:00 2001
From: tderrien <tderrien@univ-rennes1.fr>
Date: Wed, 13 Jul 2022 18:18:54 +0200
Subject: [PATCH] Set  to 1 for test file in gtf and fa

---
 scripts/FEELnc_codpot.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/FEELnc_codpot.pl b/scripts/FEELnc_codpot.pl
index 96ad36b..b975603 100755
--- a/scripts/FEELnc_codpot.pl
+++ b/scripts/FEELnc_codpot.pl
@@ -356,13 +356,13 @@
 {
     print STDERR "> Extract ORFs/cDNAs for candidates RNAs from a GTF file\n";
     # Use undef for $nbtx/$numtx to get all sequences and ORFs
-    ExtractCdnaOrf::CreateORFcDNAFromGTF($infile, $testFile, $testOrfFile, undef, undef, $genome, 'exon,CDS,stop_codon,start_codon', undef, $orfTypeTest, $verbosity, $kmerMax);
+    ExtractCdnaOrf::CreateORFcDNAFromGTF($infile, $testFile, $testOrfFile, undef, 1, $genome, 'exon,CDS,stop_codon,start_codon', undef, $orfTypeTest, $verbosity, $kmerMax);
 }
 elsif(Utils::guess_format($infile) eq "fasta") # -- if FASTA
 {
     print STDERR "> Extract ORFs/cDNAs for candidates RNAs from a FASTA file\n";
     # Use undef for $nbtx/$numtx to get all sequences and ORFs
-    ExtractCdnaOrf::CreateORFcDNAFromFASTA($infile, $testFile, $testOrfFile, undef, undef, $orfTypeTest, $verbosity, $kmerMax);
+    ExtractCdnaOrf::CreateORFcDNAFromFASTA($infile, $testFile, $testOrfFile, undef, 1, $orfTypeTest, $verbosity, $kmerMax);
 }
 else
 {