From 4992483b80c4cc1e7b28d5909b4f75cf956a9b26 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 6 Oct 2016 12:36:43 -0300
Subject: [PATCH] Change some blastx parametter to get better matches by taking
 into account intron size and the good genetic code

Former-commit-id: 6600123fbdce2070058074e82c791c7fc260c39b
Former-commit-id: ac413cc4a49844d4fa4087107aa84680d36f3df1
---
 detectors/cds/bin/do_filterbx.csh | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/detectors/cds/bin/do_filterbx.csh b/detectors/cds/bin/do_filterbx.csh
index 3dce353..77a8188 100755
--- a/detectors/cds/bin/do_filterbx.csh
+++ b/detectors/cds/bin/do_filterbx.csh
@@ -12,6 +12,9 @@ unsetenv ORG_SOURCED
 setenv ORG_HOME `dirname $0`/../../..
 source $ORG_HOME/scripts/csh_init.sh
 
+set ParamsDir = $PROG_DIR/../params
+set ModelsDir = $PROG_DIR/../models
+
 NeedArg 2
 
 set GenoFile = $Argv[1]; Shift
@@ -19,6 +22,14 @@ set ProtFile = $Argv[1]; Shift
 
 NeedFile $GenoFile
 NeedFile $ProtFile
+NeedFile $ParamsDir/default
+
+#
+# general parameters
+#
+
+source $ParamsDir/default
+
 
 set IDMIN = 70
 set NBMIN = 50
@@ -43,7 +54,9 @@ endif
 #
 
 Notify "  blasting $ProtFile"
-blastx -query $GenoFile -db $ProtFile -outfmt 7   |\
+blastx 	-query $GenoFile -db $ProtFile -outfmt 7   \
+		-query_gencode $PASS1_BLASTX_FILTER_GCODE  \
+		-max_intron_length $PASS1_MAX_INTRON      |\
   $AwkCmd -v IDMIN=$IDMIN                          \
           -v NBMIN=$NBMIN                          \
           -v NBMAX=$NBMAX                          \