chimeras

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index f45b9a87f6829b68c81c8b137758ec3f6a096022..fa9dd566c83014124fa302be6d5505102acdddac 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 = "";
-                       
+               
                        //sort parents by region start
                        sort(parents.begin(), parents.end(), compareRegionStart);
 
@@ -33,19 +33,16 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                        int longest = 0;
                        //take query and break apart into pieces using breakpoints given by results of parents
                        for (int i = 0; i < parents.size(); i++) {
-       cout << parents[i].parent << '\t' << parents[i].nastRegionStart <<  '\t' << parents[i].nastRegionEnd    << endl;        
-                               int length = parents[i].nastRegionEnd - parents[i].nastRegionStart;
+                               int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
                                string q = qAligned.substr(parents[i].nastRegionStart, length);
-       cout << "query = " << q << endl;
                                Sequence* queryFrag = new Sequence(query->getName(), q);
                                
                                queryParts.push_back(queryFrag);
-                               
+                       
                                Sequence* parent = getSequence(parents[i].parent);
                                string p = parent->getAligned();
                
                                p = p.substr(parents[i].nastRegionStart, length);
-       cout << "parent = " << p << endl;               
                                parent->setAligned(p);
                                
                                parentParts.push_back(parent);
@@ -69,7 +66,7 @@ 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()) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd);  }
-                       
+               
                        //set query to new aligned string
                        query->setAligned(newQuery);