mod to seq.error to allow for degenerate bases in the ref sequences

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index b31c4e0d89ecdb7243e9f4e42d3dc0af1d903450..af044fec3f1b60b07da406894ebc454d96df21bd 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -417,20 +417,22 @@ void SeqErrorCommand::getReferences(){
                ifstream referenceFile;
                m->openInputFile(referenceFileName, referenceFile);
                
+               int numAmbigSeqs = 0;
+               
                while(referenceFile){
                        Sequence currentSeq(referenceFile);
                        int numAmbigs = currentSeq.getAmbigBases();
-                       
-                       if(numAmbigs != 0){
-                               m->mothurOut("Warning: " + toString(currentSeq.getName()) + " has " + toString(numAmbigs) + " ambiguous bases, these bases will be removed\n");
-                               currentSeq.removeAmbigBases();
-                       }
+                       if(numAmbigs > 0){      numAmbigSeqs++; }
                        referenceSeqs.push_back(currentSeq);
                        m->gobble(referenceFile);
                }
-               numRefs = referenceSeqs.size();
-               
                referenceFile.close();
+               
+               if(numAmbigSeqs != 0){
+                       m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
+               }
+               
+               numRefs = referenceSeqs.size();
        }
        catch(exception& e) {
                m->errorOut(e, "SeqErrorCommand", "getReferences");
@@ -454,7 +456,7 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                Compare errors;
 
                for(int i=0;i<alignLength;i++){
-                       if(q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){                 //      no missing data and no double gaps
+                       if(q[i] != 'N' && q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){                  //      no missing data and no double gaps
                                started = 1;
                                
                                if(q[i] == 'A'){