X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=ae8dfb7efbb7826f40459ef87198ab72480a65ea;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=3b9d195f34fa3e916ae9b3d92328195c1337579e;hpb=cbaa068e77aeb15bb06f0695a36d8f757977ed64;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3b9d195..ae8dfb7 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -607,11 +607,10 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
 			Sequence currSeq(inFASTA); m->gobble(inFASTA);
 			//cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
-            if (m->debug) { m->mothurOut("[DEBUG]: " + toString(count) + " fasta = " + currSeq.getName() + '\n'); }
+            
 			QualityScores currQual;
 			if(qFileName != ""){
 				currQual = QualityScores(qFile);  m->gobble(qFile);
-                 if (m->debug) { m->mothurOut("[DEBUG]: qual = " + currQual.getName() + '\n'); }
 			}
 			
 			string origSeq = currSeq.getUnaligned();
@@ -883,6 +882,8 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 								 tempNameFileNames,
 								 lines[process],
 								 qLines[process]);
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
 				
 				//pass groupCounts to parent
 				if(createGroup){
@@ -1330,7 +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);
 		}