X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifyotucommand.cpp;h=f4a551cf59ffc95c587f47ea111081e0cfb6a727;hp=160928f3aa46906900ac5262f198112fb70fda36;hb=f6a58db15cdc7b90a601f8bf9c9d3b69d642f85d;hpb=7a1e4b563011b1fe4d466d64915a3cb960747125

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 160928f..f4a551c 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -544,11 +544,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 		
 		PhyloSummary* taxaSum;
         if (countfile != "") {
-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct);  }
-            else {  taxaSum = new PhyloSummary(ct); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct,false);  }
+            else {  taxaSum = new PhyloSummary(ct,false); }
 		}else {
-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap);  }
-            else {  taxaSum = new PhyloSummary(groupMap); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap,false);  }
+            else {  taxaSum = new PhyloSummary(groupMap,false); }
         }
         
         vector<ofstream*> outSums;
@@ -574,11 +574,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                 
                 PhyloSummary* taxaSumt;
                 if (countfile != "") {
-                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct);  }
-                    else {  taxaSumt = new PhyloSummary(ct); }
+                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct, false);  }
+                    else {  taxaSumt = new PhyloSummary(ct, false); }
                 }else {
-                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap);  }
-                    else {  taxaSumt = new PhyloSummary(groupMap); }
+                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap,false);  }
+                    else {  taxaSumt = new PhyloSummary(groupMap,false); }
                 }
                 taxaSums.push_back(taxaSumt);
             }