X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cooccurrencecommand.cpp;h=e4c915d6a14e4a9755a17d64c073fdda1440803b;hb=e7ae6e6b27c45b5691c19f423ec56faae8e2f255;hp=aa553b4903c10cecc582bd33dab6a130f25e4787;hpb=40b3324ee4fcb80efb3459e78efbc3140d5e739a;p=mothur.git

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index aa553b4..e4c915d 100644
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -272,6 +272,12 @@ int CooccurrenceCommand::execute(){
 int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
     try {
         int numOTUS = thisLookUp[0]->getNumBins();
+        
+        if(numOTUS < 2) {
+            m->mothurOut("Not enough OTUs for co-occurrence analysis, skipping"); m->mothurOutEndLine();
+            return 0;
+        }
+        
         vector< vector<int> > co_matrix; co_matrix.resize(thisLookUp[0]->getNumBins());
         for (int i = 0; i < thisLookUp[0]->getNumBins(); i++) { co_matrix[i].resize((thisLookUp.size()), 0); }
         vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
@@ -543,7 +549,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         
         m->mothurOut("zscore: " + toString(zscore)); m->mothurOutEndLine();
         m->mothurOut("standard deviation: " + toString(sd)); m->mothurOutEndLine();
-        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore '\t' << sd << endl;
+        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << '\t' << sd << endl;
         
         return 0;
     }