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

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index f22975ec56ed288026ca4681a223cad66b206137..6ef9532790a5fc63905cb598f1e7bc4baa4c9871 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -3069,10 +3069,9 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
                        
                                int j=4;        //need to get past the first four bases
                                while(qualities[i][j] != -1){
-                    //cout << i << '\t' << j << '\t' << qualities[i][j] << endl;
                     qualityFile << qualities[i][j] << ' ';
+                    if (j > qualities[i].size()) { break; }
                     j++;
-                    
                                }
                                qualityFile << endl;
                        }