X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=b29723c032814891f2f84dc8ba437ab789908773;hb=159fd324dfecacb6617669246d85c787ae67f630;hp=a90e7adc5c8cb870714c716b02bec5eb6bfddd73;hpb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a90e7ad..b29723c 100644
--- 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;