added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6a8afd017c1e88ff1bdbde883608b5eff00b235f..88ed32bd79bfcdc513ae4c848c775a95e762cd57 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);
+                //cout << currQual.getName() << endl;
                        }
                        
                        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)]));  }
                }       
@@ -1327,7 +1332,7 @@ 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);
                }