X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=refchimeratest.cpp;h=28e6728907470c85b97538b097180e0db71170dc;hb=0d4b21e5ccc56276b0c18d17d8e75d94ce1df4e7;hp=7af9ecd0a07ec27c65b287de98e127c53a29b513;hpb=1e4552ceb0f67f70a147d1cdca7244b62ac115ab;p=mothur.git

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 7af9ecd..28e6728 100644
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -112,9 +112,11 @@ int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left,
 	for(int i=0;i<numRefSeqs;i++){
 		
 		int lDiffs = 0;
+		
 		for(int l=0;l<alignLength;l++){
 //			if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
-			if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+						
+			if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
 				lDiffs++;
 			}
 			left[i][l] = lDiffs;
@@ -124,11 +126,12 @@ int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left,
 		int index = 0;
 		for(int l=alignLength-1;l>=0;l--){
 //			if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
-			if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+			if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
 				rDiffs++;
 			}			
 			right[i][index++] = rDiffs;
 		}
+		
 		if(lDiffs < bestSequenceMismatch){
 			bestSequenceMismatch = lDiffs;
 			bestRefSeq = i;
@@ -259,8 +262,8 @@ double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq
 	
 	for(int i=0;i<alignLength;i++){
 //		if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
-		if(chimeraRefSeq[i] != '.'){
-			if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){	/*	do nothing	*/	}
+		if(chimeraRefSeq[i] != '.' && querySeq[i] != '.'){
+			if(querySeq[i] == '-' && chimeraRefSeq[i] == '-' && chimeraRefSeq[i] != 'N'){	/*	do nothing	*/	}
 			else if(querySeq[i] == chimeraRefSeq[i]){
 				match++;
 			}