From f6d11835b89548755dc5d64ff1bd5703f5753584 Mon Sep 17 00:00:00 2001
From: pgdurand <patrick@plealog.com>
Date: Fri, 12 May 2017 09:07:27 +0200
Subject: [PATCH 1/2] fine tune program return code

---
 tools/PlastCmd.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tools/PlastCmd.cpp b/tools/PlastCmd.cpp
index 19eb22a..d6d817b 100755
--- a/tools/PlastCmd.cpp
+++ b/tools/PlastCmd.cpp
@@ -104,6 +104,7 @@ using namespace launcher::core;
 int main (int argc, char* argv[])
 {
     PlastOptionsParser parser;
+    int retcode = 0;
     try {
         /** We create a Properties instance for collecting both init properties file and user command line options. */
         IProperties* props = new Properties ();
@@ -147,20 +148,23 @@ int main (int argc, char* argv[])
     catch (OptionFailure& e)
     {
         if (parser.saw(STR_OPTION_HELP))    {   parser.displayHelp   (stdout);   }
-        else                                {   parser.displayErrors (stdout);   parser.displayHelpShort();}
+        else                                {   parser.displayErrors (stdout);   parser.displayHelpShort(); retcode = 2;}
     }
     catch (statistics::GlobalParametersFailure& e)
     {
         fprintf (stderr, MSG_MAIN_MSG2, e.getMessage());
+        retcode = 3;
     }
     catch (const char* e)
     {
         fprintf (stderr, MSG_MAIN_MSG3, e);
+        retcode = 4;
     }
     catch (...)
     {
         fprintf (stderr, "%s", MSG_MAIN_MSG4);
+        retcode = 5;
     }
 
-    return 0;
+    return retcode;
 }

From fa02be137aff404aae0042aebf9c781de2bc45fb Mon Sep 17 00:00:00 2001
From: pgdurand <patrick@plealog.com>
Date: Fri, 12 May 2017 14:49:40 +0200
Subject: [PATCH 2/2] fix order in XML element Parameters

---
 src/alignment/visitors/impl/XmlOutputVisitor.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/alignment/visitors/impl/XmlOutputVisitor.cpp b/src/alignment/visitors/impl/XmlOutputVisitor.cpp
index 3411b11..eac5a6f 100755
--- a/src/alignment/visitors/impl/XmlOutputVisitor.cpp
+++ b/src/alignment/visitors/impl/XmlOutputVisitor.cpp
@@ -144,8 +144,8 @@ void XmlOutputVisitor::visitQuerySequence (
         printline (1, "<BlastOutput_query-seq>not specified</BlastOutput_query-seq>");
         printline (1, "<BlastOutput_param>");
         printline (2, "<Parameters>");
-        printParameter(STR_OPTION_EVALUE, "expect");
         printParameter(STR_OPTION_SCORE_MATRIX, "matrix");
+        printParameter(STR_OPTION_EVALUE, "expect");
         printParameter(STR_OPTION_OPEN_GAP_COST, "gap-open");
         printParameter(STR_OPTION_EXTEND_GAP_COST, "gap-extend");
         printParameter(STR_OPTION_FILTER_QUERY, "filter");