added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 00367695944bd579c13052210b9f0d8491d0e509..ae8dfb7efbb7826f40459ef87198ab72480a65ea 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -611,7 +611,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        QualityScores currQual;
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);
-                if ((m->debug)&&(count>15800)) { m->mothurOut("[DEBUG]: " + toString(count) + " fasta = " + currSeq.getName() + '\n'); m->mothurOut("[DEBUG]: " + toString(getpid()) + '\n'); }
                        }
                        
                        string origSeq = currSeq.getUnaligned();
@@ -1332,7 +1331,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                }else if(type == "SPACER"){
                                        spacer.push_back(oligo);
                                }
-                               else{   m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
+                               else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
                        }
                        m->gobble(inOligos);
                }