X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=37beccd53455ec4f07cabb24ac88b1a3e2f28253;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=2a163516952c27f8a3dc7411536023f69e1f5b08;hpb=cd1a91833339b19a107ce769ee67b5fc74c93ce4;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 2a16351..37beccd 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -395,7 +395,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		
 		if(line->start == 0){
 			flowFile >> numFlows; m->gobble(flowFile);
-			scrapFlowFile << maxFlows << endl;
+			scrapFlowFile << numFlows << endl;
 			trimFlowFile << maxFlows << endl;
 			if(allFiles){
 				for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
@@ -599,6 +599,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 				else if(type == "REVERSE"){
 					string oligoRC = reverseOligo(oligo);
 					revPrimer.push_back(oligoRC);
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
 				}
 				else if(type == "BARCODE"){
 					oligosFile >> group;
@@ -637,8 +638,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 			primers[""] = 0;
 			primerNameVector.push_back("");			
 		}
-		
-		
+
 		outFlowFileNames.resize(barcodeNameVector.size());
 		for(int i=0;i<outFlowFileNames.size();i++){
 			outFlowFileNames[i].assign(primerNameVector.size(), "");
@@ -837,7 +837,7 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 					for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 						for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
-                                tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
+                                tempBarcodePrimerComboFileNames[i][j] += m->mothurGetpid(process) + ".temp";
                                 ofstream temp;
                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
                                 temp.close();
@@ -846,9 +846,9 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 					}
 				}
 				driverCreateTrim(flowFileName,
-								 (trimFlowFileName + toString(getpid()) + ".temp"),
-								 (scrapFlowFileName + toString(getpid()) + ".temp"),
-								 (fastaFileName + toString(getpid()) + ".temp"),
+								 (trimFlowFileName + m->mothurGetpid(process) + ".temp"),
+								 (scrapFlowFileName + m->mothurGetpid(process) + ".temp"),
+								 (fastaFileName + m->mothurGetpid(process) + ".temp"),
 								 tempBarcodePrimerComboFileNames, lines[process]);
 
 				exit(0);