optimizing classify.seqs calculating of template probabilities.

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a90e7adc5c8cb870714c716b02bec5eb6bfddd73..b29723c032814891f2f84dc8ba437ab789908773 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -704,6 +704,8 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        }
                                }
                                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + ", trashcode= " + trashCode); if (trashCode.length() != 0) { m->mothurOutEndLine(); } }
+                
                                if(trashCode.length() == 0){
                                        currSeq.setAligned(currSeq.getUnaligned());
                                        currSeq.printSequence(trimFASTAFile);
@@ -732,6 +734,8 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                                } 
                                                        }
                                                        
+                            if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
+                            
                                                        outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
                                                        
                             int numRedundants = 0;