X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.cpp;h=76d7504aa04b0170629b0f022a882be94ceacfc0;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=47b18410e6e2d61d2e58ec1b2ab170fbce34285f;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 47b1841..76d7504 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -42,7 +42,7 @@ vector<string> ClassifyOtuCommand::setParameters(){
 string ClassifyOtuCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The classify.otu command parameters are list, taxonomy, reftaxonomy, name, group, count, cutoff, label, basis and probs.  The taxonomy and list parameters are required unless you have a valid current file.\n";
+		helpString += "The classify.otu command parameters are list, taxonomy, reftaxonomy, name, group, count, persample, cutoff, label, basis and probs.  The taxonomy and list parameters are required unless you have a valid current file.\n";
 		helpString += "The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. Providing it will keep the rankIDs in the summary file static.\n";
 		helpString += "The name parameter allows you add a names file with your taxonomy file.\n";
 		helpString += "The group parameter allows you provide a group file to use in creating the summary file breakdown.\n";
@@ -53,6 +53,7 @@ string ClassifyOtuCommand::getHelpString(){
 		helpString += "Now for basis=otu could give Clostridiales	3	7	6	1	2, where 7 is the number of otus that classified to Clostridiales.\n";
 		helpString += "6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.\n";
 		helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n";
+        helpString += "The persample parameter allows you to find a consensus taxonomy for each group. Default=f\n";
 		helpString += "The default value for label is all labels in your inputfile.\n";
 		helpString += "The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy.  The default is 51, meaning 51%. Cutoff cannot be below 51.\n";
 		helpString += "The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.\n";
@@ -292,7 +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
@@ -615,9 +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;