changed groupfile in classify.seqs to reflect multiple fasta files

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index b992750f1d4fafa1374c9a8a804758cd71ba9cfc..41c321933754ebb0a86dc279985a31711b31f629 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -256,15 +256,24 @@ int FilterSeqsCommand::filterSequences() {
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               char outFilename[filteredFasta.length()];
+                               //char* outFilename = new char[filteredFasta.length()];
+                               //memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
+                               
+                               char outFilename[1024];
                                strcpy(outFilename, filteredFasta.c_str());
+
+                               //char* inFileName = new char[fastafileNames[s].length()];
+                               //memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
                                
-                               char inFileName[fastafileNames[s].length()];
+                               char inFileName[1024];
                                strcpy(inFileName, fastafileNames[s].c_str());
                                
                                MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                                MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
                                
+                               //delete inFileName;
+                               //delete outFilename;
+
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 
                                if (pid == 0) { //you are the root process 
@@ -278,8 +287,9 @@ int FilterSeqsCommand::filterSequences() {
                                        
                                        //figure out how many sequences you have to do
                                        numSeqsPerProcessor = num / processors;
-                                       if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
                                        int startIndex =  pid * numSeqsPerProcessor;
+                                       if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
+                                       
                                
                                        //do your part
                                        driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
@@ -300,8 +310,9 @@ int FilterSeqsCommand::filterSequences() {
                                        
                                        //figure out how many sequences you have to align
                                        numSeqsPerProcessor = num / processors;
-                                       if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
                                        int startIndex =  pid * numSeqsPerProcessor;
+                                       if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
+                                       
                                        
                                        //align your part
                                        driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);           
@@ -328,6 +339,8 @@ int FilterSeqsCommand::filterSequences() {
                                        
                                        lines.push_back(new linePair(0, numFastaSeqs));
                                        
+                                       numSeqs += numFastaSeqs;
+                                       
                                        driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
                                }else{
                                        setLines(fastafileNames[s]);
@@ -351,6 +364,8 @@ int FilterSeqsCommand::filterSequences() {
                                        
                                lines.push_back(new linePair(0, numFastaSeqs));
                                
+                               numSeqs += numFastaSeqs;
+                               
                                driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 
                                if (m->control_pressed) {  return 1; }
@@ -380,12 +395,13 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                
                        //read next sequence
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
-                       char buf4[length];
+                       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 seq(iss);  gobble(iss);
                        
@@ -405,11 +421,12 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                                if(count % 10 == 0){ //output to file 
                                        //send results to parent
                                        int length = outputString.length();
-                                       char buf[length];
-                                       strcpy(buf, outputString.c_str()); 
+                                       char* buf = new char[length];
+                                       memcpy(buf, outputString.c_str(), length);
                                
                                        MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
                                        outputString = "";
+                                       delete buf;
                                }
 
                        }
@@ -420,11 +437,12 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                if(outputString != ""){ //output to file 
                        //send results to parent
                        int length = outputString.length();
-                       char buf[length];
-                       strcpy(buf, outputString.c_str()); 
+                       char* buf = new char[length];
+                       memcpy(buf, outputString.c_str(), length);
                        
                        MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
                        outputString = "";
+                       delete buf;
                }
                
                if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
@@ -548,8 +566,11 @@ string FilterSeqsCommand::createFilter() {
                                MPI_Comm_size(MPI_COMM_WORLD, &processors);
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
                                                        
-                               char* tempFileName = new char(fastafileNames[s].length());
-                               tempFileName = &(fastafileNames[s][0]);
+                               //char* tempFileName = new char(fastafileNames[s].length());
+                               //tempFileName = &(fastafileNames[s][0]);
+                               
+                               char tempFileName[1024];
+                               strcpy(tempFileName, fastafileNames[s].c_str());
                
                                MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                                
@@ -565,8 +586,9 @@ string FilterSeqsCommand::createFilter() {
                                                                
                                                //figure out how many sequences you have to do
                                                numSeqsPerProcessor = num / processors;
-                                               if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
                                                int startIndex =  pid * numSeqsPerProcessor;
+                                               if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
+                                               
                                
                                                //do your part
                                                MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
@@ -582,8 +604,9 @@ string FilterSeqsCommand::createFilter() {
                                        
                                        //figure out how many sequences you have to align
                                        numSeqsPerProcessor = num / processors;
-                                       if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
                                        int startIndex =  pid * numSeqsPerProcessor;
+                                       if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
+                                       
                                        
                                        //do your part
                                        MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
@@ -692,11 +715,12 @@ string FilterSeqsCommand::createFilter() {
                MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); 
        }else{
                //recieve filterString
-               char tempBuf[alignmentLength];
+               char* tempBuf = new char[alignmentLength];
                MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
                
                filterString = tempBuf;
                if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
+               delete tempBuf; 
        }
        
        MPI_Barrier(MPI_COMM_WORLD);
@@ -764,13 +788,14 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File&
                        //read next sequence
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
        
-                       char buf4[length];
+                       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 seq(iss);  
 
                        if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }