working on pam

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 9bfdc9caba1e6bef2fe14d6eb469af2218bd29d8..d9a5e294c08d1cd3a68c7890b7c0a6ab7fbde04a 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -226,7 +226,7 @@ int ConsensusSeqsCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                if (namefile != "") { readNames(); }
-        if (countfile != "") { ct.readTable(countfile);  }
+        if (countfile != "") { ct.readTable(countfile, true, false);  }
                
                if (m->control_pressed) { return 0; }
                
@@ -312,7 +312,7 @@ int ConsensusSeqsCommand::execute(){
                
                }else {
                        
-                                               
+            
                        InputData* input = new InputData(listfile, "list");
                        ListVector* list = input->getListVector();
                        
@@ -435,6 +435,8 @@ int ConsensusSeqsCommand::processList(ListVector*& list){
                
                outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
                
+        string snumBins = toString(list->getNumBins());
+        vector<string> binLabels = list->getLabels();
                for (int i = 0; i < list->getNumBins(); i++) {
                        
                        if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
@@ -442,8 +444,8 @@ int ConsensusSeqsCommand::processList(ListVector*& list){
                        string bin = list->get(i);
                        string consSeq = getConsSeq(bin, outSummary, i);
                        
-                       outFasta << ">seq" << (i+1) << endl << consSeq << endl;
-                       outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << bin << endl;
+                       outFasta << ">" << binLabels[i] << endl << consSeq << endl;
+                       outName << binLabels[i] << '\t' << binLabels[i] << "," << bin << endl;
                }
                
                outSummary.close(); outName.close(); outFasta.close();