minor changes to pcr.seqs. Added filterToPos and filterFromPos to sequence class...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 9bda05a912551eca035bdd776387954619f5a8d8..0dc15f59ee98d0ee2d93659c4c3ad1f033f8a193 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -682,7 +682,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        if(numParentSeqs > 1 && ignoreChimeras == 1)    {       ignoreSeq = 1;  }
                        else                                                                                    {       ignoreSeq = 0;  }
                        
-                       Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
+                       Compare minCompare;
+            getErrors(query, referenceSeqs[closestRefIndex], minCompare);
                        
                        if(namesFileName != ""){
                                it = weights.find(query.getName());
@@ -839,7 +840,7 @@ void SeqErrorCommand::getReferences(){
 
 //***************************************************************************************************************
 
-Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
+int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& errors){
        try {
                if(query.getAlignLength() != reference.getAlignLength()){
                        m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
@@ -850,7 +851,7 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                string r = reference.getAligned();
 
                int started = 0;
-               Compare errors;
+               //Compare errors;
 
                for(int i=0;i<alignLength;i++){
 //                     cout << r[i] << '\t' << q[i] << '\t';
@@ -929,7 +930,8 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                errors.queryName = query.getName();
                errors.refName = reference.getName();
                
-               return errors;
+               //return errors;
+        return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "SeqErrorCommand", "getErrors");