X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.cpp;h=d9a5e294c08d1cd3a68c7890b7c0a6ab7fbde04a;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=f0fc6bff9da6d6d8b0ed8b368ad2422f25cd732a;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index f0fc6bf..d9a5e29 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -219,12 +219,14 @@ int ConsensusSeqsCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
+        int start = time(NULL);
+        
 		readFasta();
 		
 		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; }
 		
@@ -310,7 +312,7 @@ int ConsensusSeqsCommand::execute(){
 		
 		}else {
 			
-						
+            
 			InputData* input = new InputData(listfile, "list");
 			ListVector* list = input->getListVector();
 			
@@ -391,6 +393,8 @@ int ConsensusSeqsCommand::execute(){
 			delete input;
 		}
 		
+        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the consensus sequences.");
+        
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}	
@@ -431,6 +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; }
@@ -438,8 +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();