X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.cpp;h=76d7504aa04b0170629b0f022a882be94ceacfc0;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=d0ddc691236e59cdd0fcb6a2578249375fd8ad0e;hpb=7aa301dfa67cfcb5b00c6b4e38a7ad56eb8337db;p=mothur.git

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d0ddc69..76d7504 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -293,7 +293,7 @@ int ClassifyOtuCommand::execute(){
 		if (namefile != "")     {	m->readNames(namefile, nameMap, true);	}
         if (groupfile != "")    {   groupMap = new GroupMap(groupfile);  groupMap->readMap();  groups = groupMap->getNamesOfGroups(); }
         else { groupMap = NULL;  }
-        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile, true);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
         else {  ct = NULL;    }
         
 		//read taxonomy file and save in map for easy access in building bin trees
@@ -616,9 +616,10 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 			//add this bins taxonomy to summary
 			if (basis == "sequence") {
 				for(int j = 0; j < names.size(); j++) {  
-                    int numReps = 1;
-                    if (countfile != "") {  numReps = ct->getNumSeqs(names[j]); }
-                    for(int k = 0; k < numReps; k++) {  taxaSum->addSeqToTree(names[j], noConfidenceConTax);  }
+                    //int numReps = 1;
+                    //if (countfile != "") {  numReps = ct->getNumSeqs(names[j]); }
+                    //for(int k = 0; k < numReps; k++) {  taxaSum->addSeqToTree(names[j], noConfidenceConTax);  }
+                    taxaSum->addSeqToTree(names[j], noConfidenceConTax);
                 }
 			}else { //otu
                 map<string, bool> containsGroup;