added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / rarefact.cpp

diff --git a/rarefact.cpp b/rarefact.cpp
index 6a9cb3180172b8aa06aed0039d252de8bdd8873d..83a6306db7568ac228fb110f1ad1c405cec9c7ec 100644 (file)
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -86,12 +86,12 @@ int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000
                                lookup->set(binNumber, abundance);
                                rank->set(abundance, rank->get(abundance)+1);
 
-                               if((i == 0) || (i+1) % increment == 0){
+                               if((i == 0) || ((i+1) % increment == 0) || (ends.count(i+1) != 0)){
                                        rcd->updateRankData(rank);
                                }
                        }
        
-                       if(numSeqs % increment != 0){
+                       if((numSeqs % increment != 0) || (ends.count(numSeqs) != 0)){
                                rcd->updateRankData(rank);
                        }
 
@@ -123,7 +123,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
                
                //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
@@ -133,7 +133,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
                        
                                //pass numSeqs to parent
                                for(int i=0;i<displays.size();i++){
-                                       string tempFile = toString(getpid()) + toString(i) + ".rarefact.temp";
+                                       string tempFile = m->mothurGetpid(process) + toString(i) + ".rarefact.temp";
                                        displays[i]->outputTempFiles(tempFile);
                                }
                                exit(0);