finished chimera.slayer adding trim parameter, added persample parameter to sub.sampl...

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 4f48d9ce03b64ec2a5c1f52d4d3ef2feaab9d8a5..f4d04ea074b1d2d95cb9bcff4fcc3084e7f234c6 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -75,7 +75,7 @@ Bellerophon::Bellerophon(string name, bool filterSeqs,  bool c, int win, int inc
 }
 
 //***************************************************************************************************************
-int Bellerophon::print(ostream& out, ostream& outAcc) {
+int Bellerophon::print(ostream& out, ostream& outAcc, string s) {
        try {
                int above1 = 0;
                
@@ -130,7 +130,7 @@ int Bellerophon::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int Bellerophon::print(MPI_File& out, MPI_File& outAcc) {
+int Bellerophon::print(MPI_File& out, MPI_File& outAcc, string s) {
        try {
        
                int pid;
@@ -373,7 +373,11 @@ int Bellerophon::createProcesses(vector<int> mid) {
                                string tempOut = outputDir + toString(getpid()) + ".temp";
                                writePrefs(tempOut, lines[process]);
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                               exit(0);
+                       }
                }
                
                //force parent to wait until all the processes are done
@@ -531,7 +535,6 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
        try {
                
-               float dme = 0.0;
                SeqMap::iterator itR;
                SeqMap::iterator itL;