fixes while testing 1.33.0

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 82c4427fb6a9ae4c635b44d64e13a6254c351aa7..c95a1e7a4fee9efe7c821c5448fc44bf5dbd7a75 100644 (file)
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -93,7 +93,6 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<string> parents) {
                        alignmentLength = query->getAlignLength();      //x
                        int queryUnalignedLength = query->getNumBases();        //y
                        
-                       
                        buildTemplateProfile(parents);
                        
                        createAlignMatrix(queryUnalignedLength, alignmentLength);
@@ -127,7 +126,7 @@ void ChimeraReAligner::buildTemplateProfile(vector<string> parents) {
                                else if(seq[j] == 'C')  {       profile[j].C++;         }
                                else if(seq[j] == '-')  {       profile[j].Gap++;       }
                                else if(seq[j] == '.')  {       profile[j].Gap++;       }
-                               else                                    {       profile[j].A++;         }
+//                             else                                    {       profile[j].A++;         }
                                
                        }
                }
@@ -310,7 +309,7 @@ string ChimeraReAligner::getNewAlignment(string query){
                for(int i=alignmentLength-1;i>=0;i--){
                        flipSeq += queryAlignment[i];                   
                }
-               
+
                return flipSeq;
        }
        catch(exception& e) {