From: westcott <westcott>
Date: Tue, 3 May 2011 16:29:07 +0000 (+0000)
Subject: fixed id match
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=4c16a1dac0538d5ba2ac925674747ab174612ab8

fixed id match
---

diff --git a/chimerarealigner.h b/chimerarealigner.h
index 7ad7418..cf71158 100644
--- a/chimerarealigner.h
+++ b/chimerarealigner.h
@@ -25,8 +25,6 @@ class ChimeraReAligner  {
 				
 	private:
 		Sequence* querySeq;
-		
-		//Sequence* getSequence(string);  //find sequence from name
 		MothurOut* m;
 };
 /***********************************************************/
diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index e62c2f0..1f7160a 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -765,10 +765,20 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 		if (chimeraFlag == "yes") {
 		
 			if (realign) {
+				vector<Sequence*> parents;
+				for (int i = 0; i < Results.size(); i++) {
+cout << Results[i].parent  << '\t' << Results[i].nastRegionStart << '\t' << Results[i].nastRegionEnd  << endl;
+					Sequence* parent = new Sequence(Results[i].parent, Results[i].parentAligned);
+					
+					parents.push_back(parent);
+				}
+				
 				ChimeraReAligner realigner;
-				realigner.reAlign(query, Results);
+				//realigner.reAlign(query, parents);
+				
+				for (int i = 0; i < parents.size(); i++) { delete parents[i]; }
 			}
-		
+	//query->printSequence(cout);
 			//get sequence that were given from maligner results
 			vector<SeqDist> seqs;
 			map<string, float> removeDups;
@@ -1037,7 +1047,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
 		vector<int> mergedResults;
 		for (int i = 0; i < smaller.size(); i++) {
 			if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
-			
+	
 			//add left if you havent already
 			it = seen.find(smaller[i]);
 			if (it == seen.end()) {  
@@ -1065,7 +1075,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
 		}
 
 		for (int i = 0; i < mergedResults.size(); i++) {
-			
+			//cout << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl;	
 			if (db[mergedResults[i]]->getName() != q->getName()) { 
 				Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
 				refResults.push_back(temp);
diff --git a/maligner.cpp b/maligner.cpp
index 2c2cb4b..009f1e9 100644
--- 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;
diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index a055e81..73c1e5c 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -1146,7 +1146,7 @@ int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>&
 					individual += binnames[j];
 				}
 			}
-			if (subset.count(individual) != 0) {  newNames += individual;  }
+			if (subset.count(individual) != 0) {  newNames += individual + ",";  }
 			
 			
 			//if there are names in this bin add to new list