Add error if query option used in wrong place

Author: rrwick

command_line/commoncommandlinefunctions.cpp

@@ -166,6 +166,9 @@ QString checkForInvalidOrExcessSettings(QStringList * arguments)
     error = checkOptionForInt("--distance", arguments, 0, 100);
     if (error.length() > 0) return error;
 
+    if (isOptionPresent("--query", arguments) && g_settings->commandLineCommand == NO_COMMAND)
+        return "The --query option can only be used with Bandage load and Bandage image";
+
     error = checkOptionForFile("--query", arguments);
     if (error.length() > 0) return error;
     error = checkOptionForString("--blastp", arguments, QStringList(), "blastn/tblastn parameters");

program/globals.h

@@ -40,6 +40,8 @@ enum GraphFileType {LAST_GRAPH, FASTG, GFA, TRINITY, ANY_FILE_TYPE, UNKNOWN_FILE
 enum SequenceType {NUCLEOTIDE, PROTEIN, EITHER_NUCLEOTIDE_OR_PROTEIN};
 enum BlastUiState {BLAST_DB_NOT_YET_BUILT, BLAST_DB_BUILD_IN_PROGRESS, BLAST_DB_BUILT_BUT_NO_QUERIES,
                    READY_FOR_BLAST_SEARCH, BLAST_SEARCH_IN_PROGRESS, BLAST_SEARCH_COMPLETE};
+enum CommandLineCommand {NO_COMMAND, BANDAGE_LOAD, BANDAGE_IMAGE};
+
 
 extern QSharedPointer<Settings> g_settings;
 extern MyGraphicsView * g_graphicsView;

program/main.cpp

@@ -81,11 +81,13 @@ int main(int argc, char *argv[])
         if (first == "load")
         {
             arguments.pop_front();
+            g_settings->commandLineCommand = BANDAGE_LOAD;
             return bandageLoad(&a, arguments);
         }
         else if (first == "image")
         {
             arguments.pop_front();
+            g_settings->commandLineCommand = BANDAGE_IMAGE;
             return bandageImage(arguments);
         }
 //        else if (first == "contiguous")

program/settings.cpp

@@ -103,6 +103,8 @@ Settings::Settings()
     blastSearchParameters = "";
 
     rememberedPath = QDir::homePath();
+
+    commandLineCommand = NO_COMMAND;
 }
 
 

program/settings.h

@@ -113,6 +113,8 @@ class Settings
 
     QString rememberedPath;
 
+    CommandLineCommand commandLineCommand;
+
     bool anyNodeDisplayText() {return displayNodeCustomLabels || displayNodeNames || displayNodeLengths || displayNodeCoverages;}
     int getBasePairsPerSegment();
 };