#include "sequence.hpp"
#include "bayesian.h"
#include "phylotree.h"
+#include "phylosummary.h"
#include "knn.h"
//**********************************************************************************************************************
else {
//valid paramters for this command
- string AlignArray[] = {"template","fasta","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
+ string AlignArray[] = {"template","fasta","name","group","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("classify.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
}
//check for required parameters
}
else if (templateFileName == "not open") { abort = true; }
+
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true; }
else {
#endif
ifstream in;
- ableToOpen = openInputFile(fastaFileNames[i], in);
+ ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ fastaFileNames[i] = tryPath;
+ }
+ }
in.close();
#ifdef USE_MPI
#endif
if (ableToOpen == 1) {
- m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
#endif
ifstream in;
- ableToOpen = openInputFile(namefileNames[i], in);
+ ableToOpen = openInputFile(namefileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(namefileNames[i]);
+ m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ namefileNames[i] = tryPath;
+ }
+ }
in.close();
#ifdef USE_MPI
}
#endif
- if (ableToOpen == 1) { m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true; }
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
+ //erase from file list
+ namefileNames.erase(namefileNames.begin()+i);
+ i--;
+ }
+
}
}
if (namefileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a name file, you must have one for each fasta file."); m->mothurOutEndLine(); }
}
+ groupfile = validParameter.validFile(parameters, "group", false);
+ if (groupfile == "not found") { groupfile = ""; }
+ else {
+ splitAtDash(groupfile, groupfileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < groupfileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(groupfileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
+ }
+ int ableToOpen;
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ #endif
+
+ ifstream in;
+ ableToOpen = openInputFile(groupfileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(groupfileNames[i]);
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ groupfileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ #ifdef USE_MPI
+ for (int j = 1; j < processors; j++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Status status;
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
+ }
+ }
+ }
+
+ if (groupfile != "") {
+ if (groupfileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each fasta file."); m->mothurOutEndLine(); }
+ }else {
+ for (int i = 0; i < fastaFileNames.size(); i++) { groupfileNames.push_back(""); }
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
m->mothurOut("The template, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n");
m->mothurOut("The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n");
+ m->mothurOut("The group parameter allows you add a group file so you can have the summary totals broken up by group.\n");
m->mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n");
m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
m->mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n");
m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n");
- m->mothurOut("The probs parameter shut off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be run.\n");
+ m->mothurOut("The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n");
m->mothurOut("The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method. The default is 100.\n");
m->mothurOut("The classify.seqs command should be in the following format: \n");
m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+ string RippedTaxName = getRootName(getSimpleName(taxonomyFileName));
+ RippedTaxName = getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
+ if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
+ RippedTaxName += ".";
+
if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
- string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
+ string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
- string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
+ string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
outputNames.push_back(newTaxonomyFile);
outputNames.push_back(taxSummary);
#ifdef USE_MPI
int pid, end, numSeqsPerProcessor;
int tag = 2001;
- vector<long> MPIPos;
+ vector<unsigned long int> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
- char* outNewTax = new char[newTaxonomyFile.length()];\r
- memcpy(outNewTax, newTaxonomyFile.c_str(), newTaxonomyFile.length());
-
- char* outTempTax = new char[tempTaxonomyFile.length()];\r
- memcpy(outTempTax, tempTaxonomyFile.c_str(), tempTaxonomyFile.length());
+ //char* outNewTax = new char[newTaxonomyFile.length()];
+ //memcpy(outNewTax, newTaxonomyFile.c_str(), newTaxonomyFile.length());
+
+ char outNewTax[1024];
+ strcpy(outNewTax, newTaxonomyFile.c_str());
+
+ //char* outTempTax = new char[tempTaxonomyFile.length()];
+ //memcpy(outTempTax, tempTaxonomyFile.c_str(), tempTaxonomyFile.length());
+
+ char outTempTax[1024];
+ strcpy(outTempTax, tempTaxonomyFile.c_str());
- char* inFileName = new char[fastaFileNames[s].length()];\r
- memcpy(inFileName, fastaFileNames[s].c_str(), fastaFileNames[s].length());
+ //char* inFileName = new char[fastaFileNames[s].length()];
+ //memcpy(inFileName, fastaFileNames[s].c_str(), 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, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
- delete outNewTax;
- delete outTempTax;
- delete inFileName;
+ //delete outNewTax;
+ //delete outTempTax;
+ //delete inFileName;
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
-
- if(namefile != "") { MPIReadNamesFile(namefileNames[s]); }
if (pid == 0) { //you are the root process
MPIPos = setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
- MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
- MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
//figure out how many sequences you have to align
numSeqsPerProcessor = numFastaSeqs / processors;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
}
}else{ //you are a child process
- MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numFastaSeqs+1);
- MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = numFastaSeqs / processors;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
MPI_File_close(&inMPI);
MPI_File_close(&outMPINewTax);
MPI_File_close(&outMPITempTax);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- //read namefile
- if(namefile != "") {
- nameMap.clear(); //remove old names
-
- ifstream inNames;
- openInputFile(namefileNames[s], inNames);
-
- string firstCol, secondCol;
- while(!inNames.eof()) {
- inNames >> firstCol >> secondCol; gobble(inNames);
- nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
- }
- inNames.close();
- }
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
ifstream inFASTA;
openInputFile(fastaFileNames[s], inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ getNumSeqs(inFASTA, numFastaSeqs);
inFASTA.close();
lines.push_back(new linePair(0, numFastaSeqs));
driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
}
else{
- vector<int> positions;
+ vector<unsigned long int> positions;
processIDS.resize(0);
ifstream inFASTA;
while(!inFASTA.eof()){
input = getline(inFASTA);
if (input.length() != 0) {
- if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
}
}
inFASTA.close();
numFastaSeqs = positions.size();
int numSeqsPerProcessor = numFastaSeqs / processors;
-
+
for (int i = 0; i < processors; i++) {
- int startPos = positions[ i * numSeqsPerProcessor ];
+ unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
if(i == processors - 1){
numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
}
#else
ifstream inFASTA;
openInputFile(fastaFileNames[s], inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ getNumSeqs(inFASTA, numFastaSeqs);
inFASTA.close();
lines.push_back(new linePair(0, numFastaSeqs));
#endif
#endif
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ start = time(NULL);
+
+
#ifdef USE_MPI
if (pid == 0) { //this part does not need to be paralellized
+
+ if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush(); MPIReadNamesFile(namefileNames[s]); m->mothurOut(" Done."); m->mothurOutEndLine(); }
+ #else
+ //read namefile
+ if(namefile != "") {
+
+ m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
+
+ nameMap.clear(); //remove old names
+
+ ifstream inNames;
+ openInputFile(namefileNames[s], inNames);
+
+ string firstCol, secondCol;
+ while(!inNames.eof()) {
+ inNames >> firstCol >> secondCol; gobble(inNames);
+
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+
+ nameMap[firstCol] = temp;
+ }
+ inNames.close();
+
+ m->mothurOut(" Done."); m->mothurOutEndLine();
+ }
#endif
- //make taxonomy tree from new taxonomy file
- PhyloTree taxaBrowser;
+ string group = "";
+ if (groupfile != "") { group = groupfileNames[s]; }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
+ PhyloSummary taxaSum(taxonomyFileName, group);
- ifstream in;
- openInputFile(tempTaxonomyFile, in);
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
- //read in users taxonomy file and add sequences to tree
- string name, taxon;
- while(!in.eof()){
- in >> name >> taxon; gobble(in);
+ if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
+ else {
+ ifstream in;
+ openInputFile(tempTaxonomyFile, in);
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(tempTaxonomyFile.c_str()); delete classify; return 0; }
+ //read in users taxonomy file and add sequences to tree
+ string name, taxon;
- if (namefile != "") {
+ while(!in.eof()){
+ in >> name >> taxon; gobble(in);
+
itNames = nameMap.find(name);
if (itNames == nameMap.end()) {
m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
}else{
- for (int i = 0; i < itNames->second; i++) {
- taxaBrowser.addSeqToTree(name+toString(i), taxon); //add it as many times as there are identical seqs
+ for (int i = 0; i < itNames->second.size(); i++) {
+ taxaSum.addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
}
+ itNames->second.clear();
+ nameMap.erase(itNames->first);
}
- }else { taxaBrowser.addSeqToTree(name, taxon); } //add it once
+ }
+ in.close();
}
- in.close();
-
- taxaBrowser.assignHeirarchyIDs(0);
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(tempTaxonomyFile.c_str()); delete classify; return 0; }
-
- taxaBrowser.binUnclassified();
-
remove(tempTaxonomyFile.c_str());
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
-
//print summary file
ofstream outTaxTree;
openOutputFile(taxSummary, outTaxTree);
- taxaBrowser.print(outTaxTree);
+ taxaSum.print(outTaxTree);
outTaxTree.close();
//output taxonomy with the unclassified bins added
openOutputFile(unclass, outTax);
//get maxLevel from phylotree so you know how many 'unclassified's to add
- int maxLevel = taxaBrowser.getMaxLevel();
+ int maxLevel = taxaSum.getMaxLevel();
//read taxfile - this reading and rewriting is done to preserve the confidence scores.
+ string name, taxon;
while (!inTax.eof()) {
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
remove(newTaxonomyFile.c_str());
rename(unclass.c_str(), newTaxonomyFile.c_str());
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
#ifdef USE_MPI
}
#endif
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
-
-
- m->mothurOutEndLine();
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
}
delete classify;
for(int i=0;i<line->numSeqs;i++){
if (m->control_pressed) { return 0; }
-
- Sequence* candidateSeq = new Sequence(inFASTA);
-
+
+ Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+
if (candidateSeq->getName() != "") {
taxonomy = classify->getTaxonomy(candidateSeq);
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<long>& MPIPos){
+int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
try {
MPI_Status statusNew;
MPI_Status statusTemp;
}
int length = outputString.length();
- char* buf2 = new char[length];\r
+ char* buf2 = new char[length];
memcpy(buf2, outputString.c_str(), length);
MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
length = outputString.length();
- char* buf = new char[length];\r
+ char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
MPI_Offset size;
MPI_Status status;
- char* inFileName = new char[nameFilename.length()];\r
- memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
+ //char* inFileName = new char[nameFilename.length()];
+ //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, nameFilename.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
MPI_File_get_size(inMPI, &size);
- delete inFileName;
+ //delete inFileName;
char* buffer = new char[size];
MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
string firstCol, secondCol;
while(!iss.eof()) {
iss >> firstCol >> secondCol; gobble(iss);
- nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
+
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+
+ nameMap[firstCol] = temp;
}
MPI_File_close(&inMPI);
projects / mothur.git / blobdiff