X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=5800cde2146f108ae6efc3d1bce50b9bb9913750;hb=cac38e9e251998fa0b825d00189534534948d226;hp=aebb16b42a6455693b7c491f83b1740c58acd0e0;hpb=ac663461b19ad1436a06aa63f97221d1ff105482;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index aebb16b..5800cde 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++){
@@ -435,7 +435,11 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 				success = 0;
 				trashCode += 'l';
 			}
-			
+            if(!flowData.hasGoodHomoP()){	//screen to see if sequence meets the maximum homopolymer limit
+				success = 0;
+				trashCode += 'h';
+			}
+
 			int primerIndex = 0;
 			int barcodeIndex = 0;
 			
@@ -595,6 +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;
@@ -633,8 +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(), "");
@@ -821,7 +825,7 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
-			int pid = fork();
+			pid_t pid = fork();
 			
 			if (pid > 0) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
@@ -833,7 +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();
@@ -842,9 +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);