fixed id match

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 2c2cb4bb30decaed945ba21e7bbdb171c86f817f..009f1e923c9fd7449a70409867e4cffe8bc7763b 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -98,7 +98,7 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                int traceStart = trace[0].col;
                int traceEnd = trace[trace.size()-1].oldCol;    
                string queryInRange = query->getAligned();
-               queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+               queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));
                
                if (m->control_pressed) { return chimera;  }
                
@@ -118,20 +118,20 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                        temp.regionEnd = regionEnd;
                        
                        string parentInRange = refSeqs[seqIndex]->getAligned();
-                       parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1));
+                       parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart));
                        
                        temp.queryToParent = computePercentID(queryInRange, parentInRange);
                        temp.divR = (percentIdenticalQueryChimera / temp.queryToParent);
 
                        string queryInRegion = query->getAligned();
-                       queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart+1));
+                       queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart));
                        
                        string parentInRegion = refSeqs[seqIndex]->getAligned();
-                       parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1));
+                       parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart));
                        
                        temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
                        
-                       //cout << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl;
+                       cout << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl;
                        outputResults.push_back(temp);
                }
                
@@ -585,19 +585,32 @@ float Maligner::computePercentID(string queryAlign, string chimera) {
                        return -1.0;
                }
 
-       
-               int numBases = 0;
                int numIdentical = 0;
-       
+               int countA = 0;
+               int countB = 0;
                for (int i = 0; i < queryAlign.length(); i++) {
-                       if ((isalpha(queryAlign[i])) || (isalpha(chimera[i])))  {
-                               numBases++;             
-                               if (queryAlign[i] == chimera[i]) {
-                                       numIdentical++;
+                       if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
+                               ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
+                       else {
+
+                               bool charA = false; bool charB = false;
+                               if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
+                               if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
+                                       
+                               if (charA || charB) {
+                                               
+                                       if (charA) { countA++; }
+                                       if (charB) { countB++; }
+                                               
+                                       if (queryAlign[i] == chimera[i]) {
+                                               numIdentical++;
+                                       }
                                }
                        }
                }
-       
+               
+               float numBases = (countA + countB) /(float) 2;
+               
                if (numBases == 0) { return 0; }
        
                float percentIdentical = (numIdentical/(float)numBases) * 100;