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

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6a8afd017c1e88ff1bdbde883608b5eff00b235f..00367695944bd579c13052210b9f0d8491d0e509 100644 (file)
--- 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)]));  }
                }