Merge branch 'v2.3' of git+ssh://scm.gforge.inria.fr/gitroot/plast-li…

…brary/plast-library into v2.3
PLAST-software · May 16, 2017 · 40ff11e · 40ff11e
2 parents e943a6d + fa02be1
commit 40ff11e
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git 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");

diff --git 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;
 }