From: pschloss <pschloss>
Date: Thu, 5 May 2011 21:45:48 +0000 (+0000)
Subject: chimera.slayer debugging
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=ed4fc0b4ae476621747d9bfdce733e878e040e2f

chimera.slayer debugging
---

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 826f38b..1d22bdf 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -782,7 +782,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 				realigner.reAlign(query, parents);
 
 			}
-
+			
 			//get sequence that were given from maligner results
 			vector<SeqDist> seqs;
 			map<string, float> removeDups;
@@ -792,14 +792,20 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 			for (int j = 0; j < Results.size(); j++) {
 				float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal;
 				//only add if you are not a duplicate
-				itDup = removeDups.find(Results[j].parent);
-				if (itDup == removeDups.end()) { //this is not duplicate
-					removeDups[Results[j].parent] = dist;
-					parentNameSeq[Results[j].parent] = Results[j].parentAligned;
-				}else if (dist > itDup->second) { //is this a stronger number for this parent
-					removeDups[Results[j].parent] = dist;
-					parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+
+				if(Results[j].queryToParentLocal >= 90){	//local match has to be over 90% similarity
+				
+					itDup = removeDups.find(Results[j].parent);
+					if (itDup == removeDups.end()) { //this is not duplicate
+						removeDups[Results[j].parent] = dist;
+						parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+					}else if (dist > itDup->second) { //is this a stronger number for this parent
+						removeDups[Results[j].parent] = dist;
+						parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+					}
+				
 				}
+				
 			}
 			
 			for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
@@ -809,7 +815,6 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 				SeqDist member;
 				member.seq = seq;
 				member.dist = itDup->second;
-				
 				seqs.push_back(member);
 			}
 			
diff --git a/slayer.cpp b/slayer.cpp
index 877f241..61b7b63 100644
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -18,6 +18,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 		vector<data_struct> all; all.clear();
 		myQuery = *query;
 		
+				
 		for (int i = 0; i < refSeqs.size(); i++) {
 		
 			for (int j = i+1; j < refSeqs.size(); j++) {
@@ -153,8 +154,8 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
 			float QRA = computePercentID(query, parentA, breakpoint+1, length);
 		
 			float LAB = computePercentID(parentA, parentB, 0, breakpoint);
-			float RAB = computePercentID(parentA, parentB, breakpoint+1, length);
-					
+			float RAB = computePercentID(parentA, parentB, breakpoint+1, length);	
+			
 			float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 			float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 			float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
@@ -168,6 +169,7 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
 			float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 			float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 			
+			
 			//cout << q->getName() << '\t';
 			//cout << pA->getName() << '\t';
 			//cout << pB->getName() << '\t';
@@ -216,6 +218,7 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
 			}//if
 		}//for
 		
+		
 		return data;
 		
 	}