X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=508e2a90610d1b3705972a976580d90937358427;hb=ccf2fedbb600a362777a11501bb56c9c7746068e;hp=e6b00bac1361284bd803c5ffc92dfcec27e44f8e;hpb=ece154e5d02f83d0ba6bf0438e3e1f085a2920bd;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index e6b00ba..508e2a9 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -136,7 +136,7 @@ ShhherCommand::ShhherCommand(string option) {
 			flowFileName = validParameter.validFile(parameters, "flow", true);
 			flowFilesFileName = validParameter.validFile(parameters, "file", true);
 			if (flowFileName == "not found" && flowFilesFileName == "not found") {
-				m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
+				m->mothurOut("values for either flow or file must be provided for the shhh.flows command.");
 				m->mothurOutEndLine();
 				abort = true; 
 			}
@@ -152,11 +152,11 @@ ShhherCommand::ShhherCommand(string option) {
                 string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
                 
 				//flow.files = 9 character offset
-				compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+				compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
 				m->openOutputFile(compositeFASTAFileName, temp);
 				temp.close();
 				
-				compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+				compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
 				m->openOutputFile(compositeNamesFileName, temp);
 				temp.close();
 			}
@@ -218,7 +218,7 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
-                outputDir += m->hasPath(flowFileName);
+                if (outputDir == "") { outputDir = m->hasPath(flowFileName); }
                 flowFileVector.push_back(flowFileName);
             }
 		
@@ -2983,7 +2983,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
 	
 	try {
 		string thisOutputDir = outputDir;
-		if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+		if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
 		string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.qual";
         
 		ofstream qualityFile;
@@ -3091,7 +3091,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
 void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string filename, vector<int> otuCounts, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& centroids){
 	try {
 		string thisOutputDir = outputDir;
-		if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+		if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
 		string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.fasta";
 		ofstream fastaFile;
 		m->openOutputFile(fastaFileName, fastaFile);
@@ -3139,7 +3139,7 @@ void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTU
 void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string filename, vector<int> otuCounts, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU){
 	try {
 		string thisOutputDir = outputDir;
-		if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+		if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
 		string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.names";
 		ofstream nameFile;
 		m->openOutputFile(nameFileName, nameFile);
@@ -3177,7 +3177,7 @@ void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, s
 void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& seqNameVector){
 	try {
 		string thisOutputDir = outputDir;
-		if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+		if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
 		string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(filename));
 		string groupFileName = fileRoot + "shhh.groups";
 		ofstream groupFile;
@@ -3202,7 +3202,7 @@ void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& se
 void ShhherCommand::writeClusters(string filename, int numOTUs, int numFlowCells, vector<int> otuCounts, vector<int>& centroids, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU, vector<int>& lengths, vector<short>& flowDataIntI){
 	try {
 		string thisOutputDir = outputDir;
-		if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+		if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
 		string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.counts";
 		ofstream otuCountsFile;
 		m->openOutputFile(otuCountsFileName, otuCountsFile);