From 9049191e7a0be4c8bb3d79926367a7c01c636121 Mon Sep 17 00:00:00 2001
From: BenoitMorel <morelbt@hitssv543.villa-bosch.de>
Date: Thu, 5 Oct 2023 14:05:16 +0200
Subject: [PATCH] Change the logs

---
 src/ale/AleArguments.cpp |  2 +-
 src/ale/AleArguments.hpp |  2 +-
 src/ale/ale.cpp          | 11 ++++++++---
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/ale/AleArguments.cpp b/src/ale/AleArguments.cpp
index 36cc91e..2ceee38 100644
--- a/src/ale/AleArguments.cpp
+++ b/src/ale/AleArguments.cpp
@@ -37,7 +37,7 @@ AleArguments::AleArguments(int iargc, char * iargv[]):
   maxCladeSplitRatio(DEFAULT_MAX_SPLIT_RATIO),
   sampleFrequency(1),
   geneTreeSamples(DEFAULT_GENE_TREE_SAMPLES),
-  output("GeneTegrator"),
+  output("alerax_output"),
   cleanupCCP(true),
   seed(123),
   randomSpeciesRoot(false),
diff --git a/src/ale/AleArguments.hpp b/src/ale/AleArguments.hpp
index a56b83f..a2abc58 100644
--- a/src/ale/AleArguments.hpp
+++ b/src/ale/AleArguments.hpp
@@ -33,8 +33,8 @@ class AleArguments {
   std::string fractionMissingFile;
   std::string speciesCategoryFile;
   bool perFamilyRates;
-  bool memorySavings;
   bool perSpeciesRates;
+  bool memorySavings;
   double d;
   double l;
   double t;
diff --git a/src/ale/ale.cpp b/src/ale/ale.cpp
index cb39b1a..21c8362 100644
--- a/src/ale/ale.cpp
+++ b/src/ale/ale.cpp
@@ -13,6 +13,8 @@
 #include <routines/SlavesMain.hpp>
 #include <IO/HighwayCandidateParser.hpp>
 
+const char *version = "AleRax v1.0.0";
+
 void filterInvalidFamilies(Families &families)
 {
   Logger::timed << "Filtering families" << std::endl;
@@ -218,6 +220,11 @@ void run( AleArguments &args)
   std::string ccpDir = FileSystem::joinPaths(args.output, "ccps");
   FileSystem::mkdir(ccpDir, true);
   Logger::initFileOutput(FileSystem::joinPaths(args.output, "alerax"));
+  
+  Logger::timed << version << std::endl; 
+  args.printCommand();
+  args.printSummary();
+  
   auto families = FamiliesFileParser::parseFamiliesFile(args.families);
   if (!args.skipFamilyFiltering) {
     filterInvalidFamilies(families);
@@ -354,10 +361,8 @@ int genetegrator_main(int argc, char** argv, void* comm)
 {
   ParallelContext::init(comm); 
   Logger::init();
-  Logger::timed << "AleRax v1.0.0" << std::endl; 
+  Logger::timed << version << std::endl; 
   AleArguments args(argc, argv); 
-  args.printCommand();
-  args.printSummary();
   args.checkValid();
   run(args);
   Logger::close();