X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=d7731facce712bb98fd239793cda78dfa7cc69cc;hb=2405cc589aaaf0c44809a48fe98d3b96863dac0b;hp=5ffba329d31fb3e684feef6f664957ef55ec0a68;hpb=ea67d144345462d2a0ed8633c0b14f6cec8cb36e;p=mothur.git

diff --git a/maligner.cpp b/maligner.cpp
index 5ffba32..d7731fa 100644
--- 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;
 		
 	}