X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=4e5abc95b7189bd8d5178fae77c00ac17117311d;hb=HEAD;hp=5879241372dd3b60b34683683a0c1edbcbd64d57;hpb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5879241..4e5abc9 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -358,7 +358,7 @@ int SeqErrorCommand::execute(){
 		if(namesFileName != "")     {	weights = getWeights();         }
         else if (countfile != "")   {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             weights = ct.getNameMap();
         }
 		
@@ -430,13 +430,6 @@ int SeqErrorCommand::execute(){
 		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
 		m->mothurOutEndLine();
 		
-        //set fasta file as new current fastafile
-		string current = "";
-		itTypes = outputTypes.find("errorseq");
-		if (itTypes != outputTypes.end()) {
-			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
-		}
-        
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
@@ -462,18 +455,18 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 		
 		//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
 				process++;
 			}else if (pid == 0){
 				
-				num = driver(filename, qFileName, rFileName, summaryFileName + toString(getpid()) + ".temp", errorOutputFileName+ toString(getpid()) + ".temp", chimeraOutputFileName + toString(getpid()) + ".temp", lines[process], qLines[process], rLines[process]);
+				num = driver(filename, qFileName, rFileName, summaryFileName + m->mothurGetpid(process) + ".temp", errorOutputFileName+ m->mothurGetpid(process) + ".temp", chimeraOutputFileName + m->mothurGetpid(process) + ".temp", lines[process], qLines[process], rLines[process]);
 				
 				//pass groupCounts to parent
 				ofstream out;
-				string tempFile = filename + toString(getpid()) + ".info.temp";
+				string tempFile = filename + m->mothurGetpid(process) + ".info.temp";
 				m->openOutputFile(tempFile, out);
 				
 				//output totalBases and totalMatches