X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shhhseqscommand.cpp;h=82d956189a6f025fd57dc7e901e585456f59f8ab;hp=5c6359ec58bb776ce9a050a132e8409e60cf197b;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=91a27e0483827c06c21c4fe89558923bbfe86573

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 5c6359e..82d9561 100644
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -14,13 +14,13 @@
 //**********************************************************************************************************************
 vector<string> ShhhSeqsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-		CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(psigma);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-map",false,true,true); parameters.push_back(pfasta);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","name",false,true,true); parameters.push_back(pname);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+		CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(psigma);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -54,6 +54,24 @@ string ShhhSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ShhhSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta")            {   pattern = "[filename],shhh_seqs.fasta";   }
+        else if (type == "name")    {   pattern = "[filename],shhh_seqs.names";   }
+        else if (type == "map")        {   pattern = "[filename],shhh_seqs.map";   }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ShhhSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 
 ShhhSeqsCommand::ShhhSeqsCommand(){	
@@ -184,10 +202,13 @@ int ShhhSeqsCommand::execute() {
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it				
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
-		string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.names";
-		string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.map";
+		if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it		
+		
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+		string outputFileName = getOutputFileName("fasta",variables);
+		string nameFileName = getOutputFileName("name",variables);
+		string mapFileName = getOutputFileName("map",variables);
 		
 		if (groupfile != "") {
 			//Parse sequences by group
@@ -453,6 +474,9 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
 		
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
 			for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
 				mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
 			}