fixed problem with chimera.slayer realigner

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 9a25162bd60fcd35b25c18073947f1a8f6502673..a07e43392a1d96727d4870154bccef452119755b 100644 (file)
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -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);
@@ -55,10 +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
+                               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;
+                                       Nast nast(alignment, queryParts[i], parentParts[i]);
+                                       delete alignment;
+                               }
                        }
 
                        //recombine pieces to form new query sequence
@@ -78,7 +81,7 @@ 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);