more chimera.slayer debugging

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 1205cef5e36b8bb4381f5ae8bb516c30e934318d..0cd8336c6de865d85d0fea9d607199599f10ab9e 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -144,8 +144,8 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                        temp.parentAligned = db[seqIndex]->getAligned();
                        temp.nastRegionStart = spotMap[regionStart];
                        temp.nastRegionEnd = spotMap[regionEnd];
-                       temp.regionStart = regionStart;
-                       temp.regionEnd = regionEnd;
+                       temp.regionStart = unalignedMap[regionStart];
+                       temp.regionEnd = unalignedMap[regionEnd];
                        
                        string parentInRange = refSeqs[seqIndex]->getAligned();
                        parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1));
@@ -280,7 +280,22 @@ void Maligner::verticalFilter(vector<Sequence*> seqs) {
                        
                        seqs[i]->setAligned(newAligned);
                }
-
+               
+               string query = seqs[seqs.size()-1]->getAligned();
+               int queryLength = query.length();
+               
+               unalignedMap.resize(queryLength, 0);
+               
+               
+               for(int i=1;i<queryLength;i++){
+                       if(query[i] != '.' && query[i] != '-'){
+                               unalignedMap[i] = unalignedMap[i-1] + 1;
+                       }
+                       else{
+                               unalignedMap[i] = unalignedMap[i-1];
+                       }
+               }
+               
                spotMap = newMap;
        }
        catch(exception& e) {
@@ -436,12 +451,13 @@ vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> >
                        }
                }
                
-//             cout << highestScore << endl;
                vector<score_struct> path;
                
                int rowIndex = highestStruct.row;
                int pos = highestStruct.col;
                int score = highestStruct.score;
+
+//             cout << rowIndex << '\t' << pos << '\t' << score << endl;
                
                while (pos >= 0 && score > 0) {
                        score_struct temp = ms[rowIndex][pos];