X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=38c097f18b8124f1dadbd657af8413fc74f895c8;hb=5553e33be3a45eee6bed2ac9a5c4ca0aa0e8d5e4;hp=bd9ff4d083a4b20fc652bd2b3f6960cba3ce235e;hpb=605ab6fa594317a38f0df7bb6797740c735b2348;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index bd9ff4d..38c097f 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -27,6 +27,7 @@ vector<string> ChimeraSlayerCommand::getValidParameters(){
 //**********************************************************************************************************************
 ChimeraSlayerCommand::ChimeraSlayerCommand(){	
 	try {
+		abort = true; calledHelp = true;
 		vector<string> tempOutNames;
 		outputTypes["chimera"] = tempOutNames;
 		outputTypes["accnos"] = tempOutNames;
@@ -63,10 +64,10 @@ vector<string> ChimeraSlayerCommand::getRequiredFiles(){
 //***************************************************************************************************************
 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -272,6 +273,9 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 			temp = validParameter.validFile(parameters, "trim", false);				if (temp == "not found") { temp = "f"; }
 			trim = m->isTrue(temp); 
 			
+			//temp = validParameter.validFile(parameters, "trimera", false);				if (temp == "not found") { temp = "f"; }
+			//trimera = m->isTrue(temp); 
+			
 			search = validParameter.validFile(parameters, "search", false);			if (search == "not found") { search = "distance"; }
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "100"; }		
@@ -307,7 +311,8 @@ void ChimeraSlayerCommand::help(){
 		#ifdef USE_MPI
 		m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 		#endif
-		m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest peice, default=F. \n");
+		m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n");
+		//m->mothurOut("The trimera parameter allows you to check both peices of a chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n");
 		m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
 		m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
 		m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
@@ -343,7 +348,7 @@ ChimeraSlayerCommand::~ChimeraSlayerCommand(){	/*	do nothing	*/	}
 int ChimeraSlayerCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		for (int s = 0; s < fastaFileNames.size(); s++) {
 				
@@ -618,6 +623,9 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
 					Sequence* trimmed = chimera->print(out, out2);
 					
 					if (trim) { trimmed->printSequence(out3); delete trimmed; }
+					
+					//do you want to check both pieces for chimeras
+					//if (trimera) {}
 				}
 			count++;
 			}
@@ -700,6 +708,9 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
 						MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 						delete buf2;
 					}
+					
+					//do you want to check both pieces for chimeras
+					//if (trimera) {}
 						
 				}
 			}