update .gitignore

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5879241372dd3b60b34683683a0c1edbcbd64d57..4e5abc95b7189bd8d5178fae77c00ac17117311d 100644 (file)
--- 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