X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=738c3241732c814d01b87052fa3cafd899c74182;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=7798a4d74f749eed04d4554c796776a58697b98b;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 7798a4d..738c324 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -249,7 +249,7 @@ int BinSeqCommand::execute(){
 		
 		//if user gave a namesfile then use it
 		if (namesfile != "") {  readNamesFile();  }
-        if (countfile != "") {  ct.readTable(countfile);  }
+        if (countfile != "") {  ct.readTable(countfile, true, false);  }
 		
 		input = new InputData(listfile, "list");
 		list = input->getListVector();
@@ -398,6 +398,7 @@ int BinSeqCommand::process(ListVector* list) {
         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
         
         //for each bin in the list vector
+        vector<string> binLabels = list->getLabels();
         for (int i = 0; i < list->size(); i++) {
             
             if (m->control_pressed) {  return 1; }
@@ -421,11 +422,11 @@ int BinSeqCommand::process(ListVector* list) {
                             }
                             if (groups.size() != 0) { groupInfo += groups[groups.size()-1]; }
                             else { groupInfo = "not found";  }
-                            name = name + "\t" + groupInfo + "\t" + toString(i+1)+ "\tNumRep=" + toString(ct.getNumSeqs(name));
+                            name = name + "\t" + groupInfo + "\t" + binLabels[i] + "\tNumRep=" + toString(ct.getNumSeqs(name));
                             out << ">" << name << endl;
                             out << sequence << endl;
                         }else {
-                            name = name + "\t" + toString(i+1) + "\tNumRep=" + toString(ct.getNumSeqs(name));
+                            name = name + "\t" + binLabels[i] + "\tNumRep=" + toString(ct.getNumSeqs(name));
                             out << ">" << name << endl;
                             out << sequence << endl;
                         }
@@ -435,7 +436,7 @@ int BinSeqCommand::process(ListVector* list) {
                     if (sequence != "not found") {
                         //if you don't have groups
                         if (groupfile == "") {
-                            name = name + "\t" + toString(i+1);
+                            name = name + "\t" + binLabels[i];
                             out << ">" << name << endl;
                             out << sequence << endl;
                         }else {//if you do have groups
@@ -444,7 +445,7 @@ int BinSeqCommand::process(ListVector* list) {
                                 m->mothurOut(name + " is missing from your group file. Please correct. ");  m->mothurOutEndLine();
                                 return 1;
                             }else{
-                                name = name + "\t" + group + "\t" + toString(i+1);
+                                name = name + "\t" + group + "\t" + binLabels[i];
                                 out << ">" << name << endl;
                                 out << sequence << endl;
                             }