X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=00367695944bd579c13052210b9f0d8491d0e509;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=6a8afd017c1e88ff1bdbde883608b5eff00b235f;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6a8afd0..0036769 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -607,9 +607,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
 			Sequence currSeq(inFASTA); m->gobble(inFASTA);
 			//cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+            
 			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();
@@ -881,6 +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){
@@ -1185,6 +1189,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
         }
         
         for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+            if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); }
 			lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
 			if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)]));  }
 		}