update .gitignore

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index c405e38060cec0db4b610c2e6c9e24a8810d7aed..282b1284c94f6208a659a5b8ea1c30b5c5cad7cc 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1414,7 +1414,8 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
         
         RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
         
-        Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); 
+        float adjust = -1.0;
+        Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest", adjust);
         string tag = cluster->getTag();
         
         double clusterCutoff = cutoff;
@@ -2069,17 +2070,17 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                
                //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(dividedFiles[process], compositeFASTAFileName + toString(getpid()) + ".temp", compositeNamesFileName  + toString(getpid()) + ".temp");
+                               num = driver(dividedFiles[process], compositeFASTAFileName + m->mothurGetpid(process) + ".temp", compositeNamesFileName  + m->mothurGetpid(process) + ".temp");
                 
                 //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = compositeFASTAFileName + toString(getpid()) + ".num.temp";
+                               string tempFile = compositeFASTAFileName + m->mothurGetpid(process) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();