X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=f7edb21f8f6586686de459800472bf9a27582467;hb=cac38e9e251998fa0b825d00189534534948d226;hp=54d3dcc5c9b6c93f267478e6491126b3aedff772;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 54d3dcc..f7edb21 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();
         }
 		
@@ -462,18 +462,18 @@ 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
@@ -1412,9 +1412,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 					string sname = "";  nameStream >> sname;
 					sname = sname.substr(1);
                     
-                    for (int i = 0; i < sname.length(); i++) {
-                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                    }
+                    m->checkName(sname);
 					
 					map<string, int>::iterator it = firstSeqNames.find(sname);
 					
@@ -1475,9 +1473,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
-                    for (int i = 0; i < sname.length(); i++) {
-                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                    }
+                    m->checkName(sname);
                     
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);