X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=filterseqscommand.cpp;h=b17d9ed6799d9c8287664cf63241b0fde01bf40e;hp=a7d42b331bc3044de372c030175da4663f9e3a9c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=91a27e0483827c06c21c4fe89558923bbfe86573

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index a7d42b3..b17d9ed 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -14,14 +14,14 @@
 //**********************************************************************************************************************
 vector<string> FilterSeqsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-		CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
-		CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
-		CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
-		CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
-		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 pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
+		CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
+		CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
+		CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
+		CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
+		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);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -57,6 +57,22 @@ string FilterSeqsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string FilterSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],filter.fasta"; } 
+        else if (type == "filter") {  pattern =  "[filename],filter"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -277,9 +293,10 @@ int FilterSeqsCommand::execute() {
 		ofstream outFilter;
 		
 		//prevent giantic file name
-		string filterFile;
-		if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
-		else {  filterFile = outputDir + filterFileName + ".filter";  }
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + filterFileName + ".";
+		if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
+		string filterFile = getOutputFileName("filter", variables);  
 		
 		m->openOutputFile(filterFile, outFilter);
 		outFilter << filter << endl;
@@ -342,7 +359,9 @@ int FilterSeqsCommand::filterSequences() {
 			
 				for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 				
-				string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+                map<string, string> variables; 
+                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
+				string filteredFasta = getOutputFileName("fasta", variables);
 #ifdef USE_MPI	
 				int pid, numSeqsPerProcessor, num; 
 				int tag = 2001;
@@ -710,6 +729,9 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, strin
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];
 		}
@@ -1157,6 +1179,9 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             F.mergeFilter(pDataArray[i]->F.getFilter());
             
 			for (int k = 0; k < alignmentLength; k++) {	 F.a[k] += pDataArray[i]->F.a[k];       }