From 6db49dab669240bb1584c51a8979070935faee2b Mon Sep 17 00:00:00 2001
From: rey jean-Francois <jean-francois.rey@univ-avignon.fr>
Date: Fri, 2 Aug 2013 09:53:14 +0200
Subject: [PATCH] bugfix arguments

---
 main_tools/ConfPass.sh               |  2 +-
 main_tools/OneScriptToRuleThemAll.sh | 18 +++++++++---------
 tools/scripts/CheckSecondPass.sh     |  6 +++---
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/main_tools/ConfPass.sh b/main_tools/ConfPass.sh
index 3d79e20..7a7d993 100755
--- a/main_tools/ConfPass.sh
+++ b/main_tools/ConfPass.sh
@@ -73,7 +73,7 @@ do
 			exit 1
 			;;
 		\?)
-			echo "BAD USAGE : unknow opton -$OPTARG"
+			echo "BAD USAGE : unknow option -$OPTARG"
 			#exit 1
 			;;
 	esac
diff --git a/main_tools/OneScriptToRuleThemAll.sh b/main_tools/OneScriptToRuleThemAll.sh
index d44dfd1..03eecfb 100755
--- a/main_tools/OneScriptToRuleThemAll.sh
+++ b/main_tools/OneScriptToRuleThemAll.sh
@@ -65,7 +65,7 @@ scoring=0
 #---------------#
 # Parse Options #
 #---------------#
-while getopts ":hDv:cf:r123CeRsa" opt
+while getopts ":hDv:cf:r123C:eRsa" opt
 do
 	case $opt in
 		h)
@@ -81,7 +81,7 @@ do
             echo -e "\t\t-1 :\tDo 1rt pass"
             echo -e "\t\t-2 :\tDo 2nd pass"
             echo -e "\t\t-3 :\tDo 3rd pass"
-            echo -e "\t\t-C :\tDo confidence pass"
+            echo -e "\t\t-C p :\tDo p confidence pass (1=all, 2 or 3)"
             echo -e "\t\t-e :\tDo exploit confidence pass (SOLR)"
             echo -e "\t\t-R :\tDo recompose res"
             echo -e "\t\t-s :\tDo scoring"
@@ -97,7 +97,7 @@ do
             RING=$RING" -c"
             ;;
         f)
-            RING=$RING" -f $OPTARG"
+            FORKS=" -f $OPTARG"
             ;;
         r)
             RING=$RING" -r"
@@ -121,7 +121,7 @@ do
             p3=1
             ;;
         C)
-            conf=1
+            conf=$OPTARG
             ;;
         e)
             exploitconf=1
@@ -157,12 +157,12 @@ if [ -e $1 ] && [ -s $1 ]
 then
     echo -e "$LORD\n"
     REP_OUT=$2/$(basename ${1%.*})
-    if [ $p1 -eq 1 ];then ${MAIN_SCRIPT_PATH}/FirstPass.sh ${RING} $1 $2;fi
-    if [ $p2 -eq 1 ];then ${MAIN_SCRIPT_PATH}/SecondPass.sh ${RING} ${REP_OUT};fi
-    if [ $conf -eq 1 ];then $p${MAIN_SCRIPT_PATH}/ConfPass.sh ${RING} ${REP_OUT} "res_p2";fi
+    if [ $p1 -eq 1 ];then ${MAIN_SCRIPT_PATH}/FirstPass.sh ${RING} ${FORKS} $1 $2;fi
+    if [ $p2 -eq 1 ];then ${MAIN_SCRIPT_PATH}/SecondPass.sh ${RING} ${FORKS} ${REP_OUT};fi
+    if [ $conf -eq 1 ] || [ $conf -eq 2 ];then $p${MAIN_SCRIPT_PATH}/ConfPass.sh ${RING} ${REP_OUT} "res_p2";fi
     if [ $exploitconf -eq 1 ]; then ${MAIN_SCRIPT_PATH}/ExploitConfidencePass.sh ${RING} ${REP_OUT};fi
-    if [ $p3 -eq 1 ];then ${MAIN_SCRIPT_PATH}/ThirdPass.sh ${RING} ${REP_OUT};fi
-    if [ $conf -eq 1 ];then ${MAIN_SCRIPT_PATH}/ConfPass.sh ${RING} ${REP_OUT} "res_p3";fi
+    if [ $p3 -eq 1 ];then ${MAIN_SCRIPT_PATH}/ThirdPass.sh ${RING} ${FORKS} ${REP_OUT};fi
+    if [ $conf -eq 1 ] || [ $conf -eq 3 ];then ${MAIN_SCRIPT_PATH}/ConfPass.sh ${RING} ${REP_OUT} "res_p3";fi
     if [ $recompose -eq 1 ];then ${MAIN_SCRIPT_PATH}/RecomposePass.sh ${RING} ${REP_OUT};fi
     if [ $scoring -eq 1 ];then ${MAIN_SCRIPT_PATH}/ScoringRes.sh ${RING} ${REP_OUT};fi
     echo "done"
diff --git a/tools/scripts/CheckSecondPass.sh b/tools/scripts/CheckSecondPass.sh
index 2017a58..cd0e167 100644
--- a/tools/scripts/CheckSecondPass.sh
+++ b/tools/scripts/CheckSecondPass.sh
@@ -20,9 +20,9 @@ function check_second_pass_output_speeral()
     if [ $# -eq 2 ]
     then
         if [ ! -e "$1" ] || [ -z "$1" ]; then return 1; fi
-        FILENBSEG=$(ls "$2/*.seg" | grep -f "$1" | wc -l)
-        FILENBRES=$(ls "$2/*.res" | grep -f "$1" | wc -l)
-        FILENBTREIL=$(ls "$2/*.treil" | grep -f "$1" | wc -l)
+        FILENBSEG=$(ls "$2/*.seg" 2> /dev/null | grep -f "$1" | wc -l)
+        FILENBRES=$(ls "$2/*.res" 2> /dev/null | grep -f "$1" | wc -l)
+        FILENBTREIL=$(ls "$2/*.treil" 2 /dev/null | grep -f "$1" | wc -l)
         FILENB=$(cat "$1" | wc -l)    
         if [ $FILENB -ne $FILENBSEG ] || [ $FILENB -ne $FILENBRES ] || [ $FILENB -ne $FILENBTREIL ] ; then return 1;fi
     fi
-- 
1.8.2.3