mods to seq.errror

[mothur.git] / refchimeratest.cpp

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index e540d8a255363cc980318b2edf1c97bd4adcd722..4d4a658fe471ba9d0970fbb7fa57151d93c53807 100644 (file)
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -30,7 +30,7 @@ RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileN
        
        alignLength = referenceSeqs[0].length();
 
-       chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents";
+       chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
 //     chimeraReportFile << "leftParentTri,middleParentTri,rightParentTri\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
 
 }
@@ -111,7 +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;
@@ -120,7 +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;
@@ -254,7 +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++;