+//**********************************************************************************************************************
+vector<string> ChimeraSlayerCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta", "processors", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
+ "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChimeraSlayerCommand::ChimeraSlayerCommand(){
+ try {
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraSlayerCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"template","fasta"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraSlayerCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "getRequiredFiles");
+ exit(1);
+ }
+}