update .gitignore

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d196db85e3da3fabf72307f47ac58996833b6457..4e5abc95b7189bd8d5178fae77c00ac17117311d 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -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(); }
@@ -462,7 +455,7 @@ 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