X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.cpp;h=a07e43392a1d96727d4870154bccef452119755b;hb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;hp=1da327819ab446fe62fb965f36b48211d484b97e;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 1da3278..a07e433 100644
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -24,7 +24,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			
 			string qAligned = query->getAligned();
 			string newQuery = "";
-			
+		
 			//sort parents by region start
 			sort(parents.begin(), parents.end(), compareRegionStart);
 
@@ -34,9 +34,9 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 
 			//take query and break apart into pieces using breakpoints given by results of parents
 			for (int i = 0; i < parents.size(); i++) {
-			
 				int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
 				string q = qAligned.substr(parents[i].nastRegionStart, length);
+	
 				Sequence* queryFrag = new Sequence(query->getName(), q);
 
 				queryParts.push_back(queryFrag);
@@ -55,9 +55,13 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 
 			//align each peice to correct parent from results
 			for (int i = 0; i < queryParts.size(); i++) {
-				alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
-				Nast nast(alignment, queryParts[i], parentParts[i]);
-				delete alignment;
+				if ((queryParts[i]->getUnaligned() == "") || (parentParts[i]->getUnaligned() == "")) {;}
+				else {
+					alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+				
+					Nast nast(alignment, queryParts[i], parentParts[i]);
+					delete alignment;
+				}
 			}
 
 			//recombine pieces to form new query sequence
@@ -77,10 +81,10 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			
 			//make sure you don't cutoff end of query 
 			if (parents[parents.size()-1].nastRegionEnd < (qAligned.length()-1)) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd+1);  }
-		
+			
 			//set query to new aligned string
 			query->setAligned(newQuery);
-			
+
 			//free memory
 			for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i];  }
 			for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i];  }