X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=729ef1f854fa445aed5a84b5ca5b90a3b2255aaa;hb=d945488119ad368b180537f36ed40298ff170f39;hp=423f7c0e713eef53a8904c2dcaff49a35844f35f;hpb=3489799717f1f9002846bfd902d2886fc448f903;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 423f7c0..729ef1f 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -773,7 +773,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 		for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];	}
 		
 		if (chimeraFlag == "yes") {
-
+			
 			if (realign) {
 				vector<string> parents;
 				for (int i = 0; i < Results.size(); i++) {
@@ -1113,7 +1113,8 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
 				seen[tempIndexesRight[i]] = tempIndexesRight[i];
 			}
 		}
-		
+		//string qname = q->getName().substr(0, q->getName().find_last_of('_'));	
+		//cout << qname << endl;	
 		
 		for (int i = 0; i < mergedResults.size(); i++) {
 			//cout << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl;	
@@ -1201,7 +1202,6 @@ vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db,
 			}
 		}
 		
-		
 		for (int i = 0; i < mergedResults.size(); i++) {
 			//cout << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl;	
 			if (db[mergedResults[i]]->getName() != q->getName()) {