X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=c34f25de509c78b9e1b97b7c303142864e3c7e01;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=97629b600031c06c063f405175dd9fa369ae7c93;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 97629b6..c34f25d 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -802,7 +802,7 @@ string ShhherCommand::createNamesFile(){
 			duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
 		}
 		
-		string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName) + getOutputFileNameTag("name");
+		string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
 		
 		ofstream nameFile;
 		m->openOutputFile(nameFileName, nameFile);
@@ -1839,14 +1839,17 @@ void ShhherCommand::writeGroups(){
     try {
         string thisOutputDir = outputDir;
         if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-        string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
-        string groupFileName = fileRoot + getOutputFileNameTag("group");
+        string fileRoot = m->getRootName(m->getSimpleName(flowFileName));
+        int pos = fileRoot.find_first_of('.');
+        string fileGroup = fileRoot;
+        if (pos != string::npos) {  fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1)));  }
+        string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
         ofstream groupFile;
         m->openOutputFile(groupFileName, groupFile);
         
         for(int i=0;i<numSeqs;i++){
             if (m->control_pressed) { break; }
-            groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
+            groupFile << seqNameVector[i] << '\t' << fileGroup << endl;
         }
         groupFile.close();
         outputNames.push_back(groupFileName);
@@ -2306,7 +2309,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 if (m->control_pressed) { break; }
                 
                 vector<int> otuCounts(numOTUs, 0);
-                for(int i=0;i<numSeqs;i++)	{	otuCounts[otuData[i]]++;	}
+                for(int j=0;j<numSeqs;j++)	{	otuCounts[otuData[j]]++;	}
                 
                 calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);	
                 
@@ -2319,15 +2322,18 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
                 string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
                 string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("counts");
-                string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
-                string groupFileName = fileRoot + getOutputFileNameTag("group");
+                string fileRoot = m->getRootName(m->getSimpleName(flowFileName));
+                int pos = fileRoot.find_first_of('.');
+                string fileGroup = fileRoot;
+                if (pos != string::npos) {  fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1)));  }
+                string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
 
                 
                 writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; }
                 writeSequences(thisCompositeFASTAFileName, numOTUs, numFlowCells, fastaFileName, otuCounts, uniqueFlowgrams, seqNameVector, aaI, centroids);if (m->control_pressed) { break; }
                 writeNames(thisCompositeNamesFileName, numOTUs, nameFileName, otuCounts, seqNameVector, aaI, nSeqsPerOTU);				if (m->control_pressed) { break; }
                 writeClusters(otuCountsFileName, numOTUs, numFlowCells,otuCounts, centroids, uniqueFlowgrams, seqNameVector, aaI, nSeqsPerOTU, lengths, flowDataIntI);			if (m->control_pressed) { break; }
-                writeGroups(groupFileName, fileRoot, numSeqs, seqNameVector);						if (m->control_pressed) { break; }
+                writeGroups(groupFileName, fileGroup, numSeqs, seqNameVector);						if (m->control_pressed) { break; }
                 
                 if (large) {
                     if (g > 0) {
@@ -2626,7 +2632,7 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
 		read->read(clusterNameMap);
         
 		ListVector* list = read->getListVector();
-		SparseMatrix* matrix = read->getMatrix();
+		SparseDistanceMatrix* matrix = read->getDMatrix();
 		
 		delete read; 
 		delete clusterNameMap;