X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=6a4732cf72cd4222e539beb93c6b0b45226d2a08;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=cc486d3ab690fd655c1de8a22ae406eafc2c242f;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index cc486d3..6a4732c 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -65,6 +65,26 @@ string ChimeraCheckCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "chimera") {  outputFileName =  "chimeracheck.chimeras"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -342,7 +362,7 @@ int ChimeraCheckCommand::execute(){
 			if (m->control_pressed) { delete chimera;	return 0;	}
 			
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
 			outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 			
 		#ifdef USE_MPI
@@ -531,6 +551,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 			
 			//report progress
 			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+            count++;
 		}
 		//report progress
 		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}