Inform when no operation is done

Author: nicodr97

include/reportsystem.h

@@ -307,6 +307,8 @@ enum InfoCode {
 
     UsingPlatform                               = 5,
 
+    OnlyReadAndWrite                            = 6,
+
 
     __MAXINFO
 };

source/reportMessages/infoMessages.cpp

@@ -47,5 +47,8 @@ const std::map<InfoCode, const char *> reporting::reportManager::InfoMessages =
                 "Removing sequence \"[tag]\" as it is a duplicate of \"[tag]\"."},
 
     {InfoCode::UsingPlatform,
-                "Using \"[tag]\" CPU extensions to compute statistics."}
+                "Using \"[tag]\" CPU extensions to compute statistics."},
+
+    {InfoCode::OnlyReadAndWrite,
+                "No filtering or calculation performed. Output same MSA as input."}
 };

source/trimalManager.cpp

@@ -314,6 +314,11 @@ int trimAlManager::parseArguments(int argc, char **argv) {
         if ((origAlig = formatManager.loadAlignment(infile)) == nullptr) {
             appearErrors = true;
         }
+
+        if ((*i) + 1 == *argc) {
+            debug.report(InfoCode::OnlyReadAndWrite);
+        }
+
         return Recognized;
     }
     return NotRecognized;