removing mallard

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 28984c6bd6f275bf40e9002d673e6a0dd360de90..53bdd9e63f396ec44c608398e54bd649dca31073 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -89,6 +89,7 @@ void Pintail::getChimeras() {
                h.resize(numSeqs);
                quantiles.resize(100);  //one for every percent mismatch
                quantilesMembers.resize(100);  //one for every percent mismatch
+               makeCompliant.resize(templateSeqs.size(), 0.0);
                
                //break up file if needed
                int linesPerProcess = numSeqs / processors ;
@@ -137,25 +138,6 @@ void Pintail::getChimeras() {
                }else {         createProcessesPairs();         }
                
                
-               for (int j = 0; j < bestfit.size(); j++) { 
-                               
-                               //chops off beginning and end of sequences so they both start and end with a base
-                               ofstream out;
-                               string s = querySeqs[j]->getName();
-                       
-                               openOutputFile(s, out);
-                               out << ">" << querySeqs[j]->getName() << endl;
-                               out << querySeqs[j]->getAligned() << endl;
-                               out.close();
-                               
-                               string t =querySeqs[j]->getName() + ".ref";
-                               openOutputFile(t, out);
-                               out << ">" << bestfit[j]->getName() << endl;
-                               out << bestfit[j]->getAligned() << endl;
-                               out.close();    
-               }
-
-               
                //find P
                mothurOut("Getting conservation... "); cout.flush();
                if (consfile == "") {