fix trim.seqs / qualscores bug

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 8a229e3cade2cff57569e16b0e4b682d8dd0be65..304848179331ab980730713c5a35998bb54a80bc 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -64,7 +64,7 @@ vector<string> AlignCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["alignreport"] = tempOutNames;
@@ -78,10 +78,10 @@ AlignCommand::AlignCommand(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
        
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true;}
                
                else {
                        
@@ -278,7 +278,7 @@ void AlignCommand::help(){
 
 int AlignCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
                int longestBase = templateDB->getLongestBase();
@@ -309,7 +309,7 @@ int AlignCommand::execute(){
                        int start = time(NULL);
                
 #ifdef USE_MPI 
-                               int pid, end, numSeqsPerProcessor; 
+                               int pid, numSeqsPerProcessor; 
                                int tag = 2001;
                                vector<unsigned long int> MPIPos;
                                MPIWroteAccnos = false;
@@ -554,7 +554,8 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        if (m->control_pressed) {  return 0; }
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
-                       
+                       report.setCandidate(candidateSeq);
+
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;
@@ -617,7 +618,6 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                                        accnosFile << candidateSeq->getName() << wasBetter << endl;
                                }
                                
-                               report.setCandidate(candidateSeq);
                                report.setTemplate(templateSeq);
                                report.setSearchParameters(search, searchScore);
                                report.setAlignmentParameters(align, alignment);
@@ -705,7 +705,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
                        istringstream iss (tempBuf,istringstream::in);
 
                        Sequence* candidateSeq = new Sequence(iss);  
-       
+                       report.setCandidate(candidateSeq);
+
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;
@@ -776,7 +777,6 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
                                        MPIWroteAccnos = true;
                                }
                                
-                               report.setCandidate(candidateSeq);
                                report.setTemplate(templateSeq);
                                report.setSearchParameters(search, searchScore);
                                report.setAlignmentParameters(align, alignment);
@@ -849,7 +849,11 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                                out.close();
                                
                                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