1.10.0

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a544733375b004e651409ef47c9db62bb0f0756d..ae9c436440950cca6cd33eb99e85c5b9b4db1062 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -266,13 +266,13 @@ int TrimSeqsCommand::execute(){
                                if (m->control_pressed) {  return 0; }
                #else
                                ifstream inFASTA;
-                               openInputFile(fastafileNames[s], inFASTA);
-                               numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               openInputFile(fastaFile, inFASTA);
+                               int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numSeqs));
                                
-                               driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+                               driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
                                
                                if (m->control_pressed) {  return 0; }
                #endif
@@ -331,7 +331,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                if (oligoFile != "") {          
                        openOutputFile(groupFile, outGroups);   
                        for (int i = 0; i < fastaNames.size(); i++) {
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+                       #else
+                               fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));                      
+                       #endif
                        }
                }
                
@@ -674,12 +678,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
                                }
                                oligo = oligo.substr(0,alnLength);
                                temp = temp.substr(0,alnLength);
-//                             cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;                     
-                               cout << seq.getName() << endl;
-                               cout << temp << endl;
-                               cout << oligo << endl;
-                               cout << alnLength << endl;
-                               cout << endl;
+//                             
                                
                                int newStart=0;
                                int numDiff = countDiffs(oligo, temp);
@@ -789,13 +788,7 @@ int TrimSeqsCommand::stripForward(Sequence& seq){
                                }
                                oligo = oligo.substr(0,alnLength);
                                temp = temp.substr(0,alnLength);
-//                             cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;                     
-                               cout << seq.getName() << endl;
-                               cout << temp << endl;
-                               cout << oligo << endl;
-                               cout << alnLength << endl;
-                               cout << endl;
-                               
+//                                                             
                                int newStart=0;
                                int numDiff = countDiffs(oligo, temp);
                                if(numDiff < minDiff){