X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=refchimeratest.cpp;h=4d4a658fe471ba9d0970fbb7fa57151d93c53807;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=246d4394a58ae7f5d65bf78c8b0d19a426ea30c6;hpb=5e5253ff472de3c6349e562d2580873287be0c65;p=mothur.git

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 246d439..4d4a658 100644
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -30,8 +30,8 @@ RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileN
 	
 	alignLength = referenceSeqs[0].length();
 
-	chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\t";
-	chimeraReportFile << "leftParentChi,middleParentTri,rightParentChi\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
+	chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
+//	chimeraReportFile << "leftParentTri,middleParentTri,rightParentTri\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
 
 }
 
@@ -54,8 +54,8 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
 	int leftParentBi, rightParentBi, breakPointBi;
 	int minMismatchToChimera = getChimera(left, right, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight);
 	
-	int minMismatchToTrimera = MAXINT;
-	int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
+//	int minMismatchToTrimera = MAXINT;
+//	int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
 	
 	int nMera = 0;
 	string chimeraRefSeq = "";
@@ -65,17 +65,20 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
 		chimeraRefSeq = referenceSeqs[bestMatch];
 	}
 	else {
-		
-		minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
 
-		if(minMismatchToChimera - minMismatchToTrimera <= 3){
-			nMera = 2;
-			chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
-		}
-		else{			
-			nMera = 3;
-			chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
-		}
+		nMera = 2;
+		chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
+		
+//		minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
+//
+//		if(minMismatchToChimera - minMismatchToTrimera <= 3){
+//			nMera = 2;
+//			chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
+//		}
+//		else{			
+//			nMera = 3;
+//			chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
+//		}
 		
 	}
 	double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
@@ -86,12 +89,12 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
 	chimeraReportFile << referenceNames[leftParentBi] << ',' << referenceNames[rightParentBi] << '\t' << breakPointBi << '\t';
 	chimeraReportFile << minMismatchToChimera << '\t';
 	
-	if(nMera == 1){
-		chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
-	}
-	else{
-		chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;	
-	}
+//	if(nMera == 1){
+//		chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
+//	}
+//	else{
+//		chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;	
+//	}
 	
 	chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
 		
@@ -108,7 +111,8 @@ int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left,
 		
 		int lDiffs = 0;
 		for(int l=0;l<alignLength;l++){
-			if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+//			if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+			if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
 				lDiffs++;
 			}
 			left[i][l] = lDiffs;
@@ -117,7 +121,8 @@ int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left,
 		int rDiffs = 0;
 		int index = 0;
 		for(int l=alignLength-1;l>=0;l--){
-			if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+//			if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+			if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
 				rDiffs++;
 			}			
 			right[i][index++] = rDiffs;
@@ -251,7 +256,8 @@ double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq
 	int mismatch = 0;
 	
 	for(int i=0;i<alignLength;i++){
-		if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
+//		if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
+		if(chimeraRefSeq[i] != '.'){
 			if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){	/*	do nothing	*/	}
 			else if(querySeq[i] == chimeraRefSeq[i]){
 				match++;