a few modifications for 1.9

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 777584bf0c75cdc8f26d5125defa5e20f296ce6e..4b309c0124a2038cb49db3980345e10e535ce84d 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -217,13 +217,13 @@ int ChimeraSlayerCommand::execute(){
                        int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                        int inMode=MPI_MODE_RDONLY; 
                        
-                       char* outFilename = new char[outputFileName.length()];\r
+                       char* outFilename = new char[outputFileName.length()];
                        memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
                        
-                       char* outAccnosFilename = new char[accnosFileName.length()];\r
+                       char* outAccnosFilename = new char[accnosFileName.length()];
                        memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
 
-                       char* inFileName = new char[fastafile.length()];\r
+                       char* inFileName = new char[fastafile.length()];
                        memcpy(inFileName, fastafile.c_str(), fastafile.length());
 
                        MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
@@ -235,7 +235,6 @@ int ChimeraSlayerCommand::execute(){
                        delete outAccnosFilename;
 
                        if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
-
                
                        if (pid == 0) { //you are the root process 
                                m->mothurOutEndLine();
@@ -246,7 +245,7 @@ int ChimeraSlayerCommand::execute(){
                                
                                //print header
                                int length = outTemp.length();
-                               char* buf2 = new char[length];\r
+                               char* buf2 = new char[length];
                                memcpy(buf2, outTemp.c_str(), length);
 
                                MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
@@ -427,7 +426,7 @@ int ChimeraSlayerCommand::execute(){
                        if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                #endif
                
-               appendFiles(tempHeader, outputFileName);
+               appendFiles(outputFileName, tempHeader);
        
                remove(outputFileName.c_str());
                rename(tempHeader.c_str(), outputFileName.c_str());
@@ -510,8 +509,7 @@ int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string file
 //**********************************************************************************************************************
 #ifdef USE_MPI
 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
-       try {
-                               
+       try {                           
                MPI_Status status; 
                int pid;
                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -522,30 +520,33 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
                        
                        //read next sequence
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
-       
+
                        char* buf4 = new char[length];
                        MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
-                       
+       
                        string tempBuf = buf4;
                        if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
                        istringstream iss (tempBuf,istringstream::in);
+
                        delete buf4;
 
                        Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
-                               
+               
                        if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
                                
                                if (candidateSeq->getAligned().length() != templateSeqsLength) {  
                                        m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
                                }else{
+               
                                        //find chimeras
                                        chimera->getChimeras(candidateSeq);
-                                       
+                       
                                        if (m->control_pressed) {       delete candidateSeq; return 1;  }
-               
+               //cout << "about to print" << endl;
                                        //print results
                                        bool isChimeric = chimera->print(outMPI, outAccMPI);
                                        if (isChimeric) { MPIWroteAccnos = true;  }
+       
                                }
                        }
                        delete candidateSeq;