X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pintail.cpp;h=7ae3ff6dbb96224197dff97db4b435880738d87b;hb=98ea55ba2d46a429f031086b4b3272780d0ec894;hp=7b99cab9e7eed714a0cefeee4b45ed8057429c6f;hpb=ec92647e652017e0cd4ba0488a815094f88373b3;p=mothur.git

diff --git a/pintail.cpp b/pintail.cpp
index 7b99cab..7ae3ff6 100644
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -146,18 +146,15 @@ void Pintail::getChimeras() {
 			mothurOut("Done."); mothurOutEndLine();
 		}else {		createProcessesPairs();		}
 		
-/*string o = "foronlinepintailpairs-eachgap";
-ofstream out7;
-openOutputFile(o, out7);
+//string o = "closestmatch.eachgap.fasta";
+//ofstream out7;
+//openOutputFile(o, out7);
 
-for (int i = 0; i < bestfit.size(); i++) {
-	out7 << querySeqs[i]->getName() << endl;
-	out7 << querySeqs[i]->getUnaligned() << endl << endl;
-	
-	out7 << bestfit[i]->getName() << endl;
-	out7 << bestfit[i]->getUnaligned() << endl << endl << endl;
-}		
-out7.close();/*/	
+//for (int i = 0; i < bestfit.size(); i++) {
+	//out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
+	//out7 << bestfit[i]->getAligned() << endl;
+//}		
+//out7.close();	
 		//find P
 		mothurOut("Getting conservation... "); cout.flush();
 		if (consfile == "") {