fixed bug in nast:removeextragaps

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 0f2556aff6983107067635fba4015f88c9e9d33a..9a25162bd60fcd35b25c18073947f1a8f6502673 100644 (file)
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -24,7 +24,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                        
                        string qAligned = query->getAligned();
                        string newQuery = "";
-       //cout << qAligned.length() << endl;            
+               
                        //sort parents by region start
                        sort(parents.begin(), parents.end(), compareRegionStart);
 
@@ -56,6 +56,7 @@ 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;
                        }
@@ -80,7 +81,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                
                        //set query to new aligned string
                        query->setAligned(newQuery);
-       //cout << newQuery.length() << endl;            
+
                        //free memory
                        for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i];  }
                        for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i];  }