chimera.slayer debugging

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 826f38ba962681e883809c5dcb2711939d205c99..1d22bdfe36f74194d2609c01b956cf0ab8ba67c8 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -782,7 +782,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                                realigner.reAlign(query, parents);
 
                        }
-
+                       
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;
@@ -792,14 +792,20 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        for (int j = 0; j < Results.size(); j++) {
                                float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal;
                                //only add if you are not a duplicate
-                               itDup = removeDups.find(Results[j].parent);
-                               if (itDup == removeDups.end()) { //this is not duplicate
-                                       removeDups[Results[j].parent] = dist;
-                                       parentNameSeq[Results[j].parent] = Results[j].parentAligned;
-                               }else if (dist > itDup->second) { //is this a stronger number for this parent
-                                       removeDups[Results[j].parent] = dist;
-                                       parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+
+                               if(Results[j].queryToParentLocal >= 90){        //local match has to be over 90% similarity
+                               
+                                       itDup = removeDups.find(Results[j].parent);
+                                       if (itDup == removeDups.end()) { //this is not duplicate
+                                               removeDups[Results[j].parent] = dist;
+                                               parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+                                       }else if (dist > itDup->second) { //is this a stronger number for this parent
+                                               removeDups[Results[j].parent] = dist;
+                                               parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+                                       }
+                               
                                }
+                               
                        }
                        
                        for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
@@ -809,7 +815,6 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                                SeqDist member;
                                member.seq = seq;
                                member.dist = itDup->second;
-                               
                                seqs.push_back(member);
                        }