chimera.slayer debugging

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 5ffba329d31fb3e684feef6f664957ef55ec0a68..d7731facce712bb98fd239793cda78dfa7cc69cc 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -97,9 +97,11 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                int traceStart = path[0].col;
                int traceEnd = path[path.size()-1].col; 
                string queryInRange = query->getAligned();
-               queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));
+               queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
                
                string chimeraSeq = constructChimericSeq(trace, refSeqs);
+//             cout << queryInRange.length() << endl;
+//             cout << chimeraSeq.length() << endl;
                
                percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
                
@@ -137,20 +139,20 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                        temp.regionEnd = regionEnd;
                        
                        string parentInRange = refSeqs[seqIndex]->getAligned();
-                       parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart));
+                       parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1));
                        
                        temp.queryToParent = computePercentID(queryInRange, parentInRange);
                        temp.divR = (percentIdenticalQueryChimera / temp.queryToParent);
 
                        string queryInRegion = query->getAligned();
-                       queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart));
+                       queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart+1));
                        
                        string parentInRegion = refSeqs[seqIndex]->getAligned();
-                       parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart));
+                       parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1));
                        
                        temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
                        
-                       //cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " <<  temp.divR << endl;
+//                     cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " <<  temp.divR << endl;
 
                        outputResults.push_back(temp);
                }
@@ -652,8 +654,9 @@ string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequenc
                        seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
                        chimera += seqAlign;
                }
-               
-               if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); }
+//             cout << chimera << endl;
+//             if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); }       //this was introducing a fence post error
+//             cout << chimera << endl;
                return chimera;
        }
        catch(exception& e) {
@@ -697,6 +700,7 @@ float Maligner::computePercentID(string queryAlign, string chimera) {
                        return -1.0;
                }
 
+//             cout << queryAlign.length() << endl;
                int numIdentical = 0;
                int countA = 0;
                int countB = 0;
@@ -709,6 +713,7 @@ float Maligner::computePercentID(string queryAlign, string chimera) {
                                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++; }
@@ -718,15 +723,22 @@ float Maligner::computePercentID(string queryAlign, string chimera) {
                                                numIdentical++;
                                        }
                                }
+//                             cout << queryAlign[i] << '\t' << chimera[i] << '\t' << countA << '\t' << countB << endl;
+
                        }
                }
                
+//             cout << "pat\t" << countA << '\t' << countB << '\t' << numIdentical << endl;
+
+               
                float numBases = (countA + countB) /(float) 2;
                
                if (numBases == 0) { return 0; }
        
                float percentIdentical = (numIdentical/(float)numBases) * 100;
-
+               
+//             cout << percentIdentical << endl;
+               
                return percentIdentical;
                
        }