some alterations to chimera.slayer

[mothur.git] / refchimeratest.cpp

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 7af9ecd0a07ec27c65b287de98e127c53a29b513..28e6728907470c85b97538b097180e0db71170dc 100644 (file)
--- 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++;
                        }