Merge remote-tracking branch 'origin/master'

[mothur.git] / removerarecommand.cpp

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index a551681fb6721e4b3670fe912e1b6bfe909dd388..c378e41447013ba021935d07e76af3ae029ad1b0 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -411,7 +411,7 @@ int RemoveRareCommand::processList(){
                        util.setGroups(Groups, namesGroups);
                        m->openOutputFile(outputGroupFileName, outGroup);
                }else if (countfile != "") {
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (ct.hasGroupInfo()) {
                 vector<string> namesGroups = ct.getNamesOfGroups();
                 SharedUtil util;
@@ -850,7 +850,7 @@ int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup){
                                
                                //eliminates zero otus
                                if (allZero) { for (int j = 0; j < newRabunds.size(); j++) {  newRabunds[j].pop_back(); } }
-                else { headers.push_back(m->currentBinLabels[i]); }
+                else { headers.push_back(m->currentSharedBinLabels[i]); }
                        }
                }else {
                        //for each otu
@@ -867,7 +867,7 @@ int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup){
                                
                                //eliminates otus below rare cutoff
                                if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) {  newRabunds[j].pop_back(); } }
-                else { headers.push_back(m->currentBinLabels[i]); }
+                else { headers.push_back(m->currentSharedBinLabels[i]); }
                        }
                }