added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3b9d195f34fa3e916ae9b3d92328195c1337579e..00367695944bd579c13052210b9f0d8491d0e509 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -607,11 +607,11 @@ 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'); }
+                if ((m->debug)&&(count>15800)) { m->mothurOut("[DEBUG]: " + toString(count) + " fasta = " + currSeq.getName() + '\n'); m->mothurOut("[DEBUG]: " + toString(getpid()) + '\n'); }
                        }
                        
                        string origSeq = currSeq.getUnaligned();
@@ -883,6 +883,8 @@ 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){