C++ OptArgs::GetLeftoverArguments方法代码示例

int IonstatsReduceH5(int argc, const char *argv[])
{
  OptArgs opts;
  opts.ParseCmdLine(argc-1, argv+1);

  string output_h5_filename = opts.GetFirstString  ('o', "output", "");
  bool merge_proton_blocks  = opts.GetFirstBoolean ('b', "merge-proton-blocks", "true");
  vector<string>  input_h5_filename;
  opts.GetLeftoverArguments(input_h5_filename);

  if(input_h5_filename.empty() or output_h5_filename.empty()) {
    IonstatsReduceH5Help();
    return 1;
  }

  if(merge_proton_blocks)
    cout << "NOTE:" << argv[0] << " " << argv[1] << ": --merge-proton-blocks=true so any Proton block-specific read group suffixes will be merged" << endl;

  return IonstatsAlignmentReduceH5(output_h5_filename, input_h5_filename, merge_proton_blocks);
}

int IonstatsReduce(int argc, const char *argv[])
{
  OptArgs opts;
  opts.ParseCmdLine(argc, argv);

  string output_json_filename = opts.GetFirstString('o', "output", "");
  vector<string>  input_jsons;
  opts.GetLeftoverArguments(input_jsons);

  if(input_jsons.empty() or output_json_filename.empty()) {
    IonstatsReduceHelp();
    return 1;
  }

  ifstream in(input_jsons[0].c_str(), ifstream::in);
  if (!in.good()) {
    fprintf(stderr, "[ionstats] ERROR: cannot open %s\n", input_jsons[0].c_str());
    return 1;
  }
  Json::Value first_input_json;
  in >> first_input_json;
  in.close();

  if (!first_input_json.isMember("meta")) {
    fprintf(stderr, "[ionstats] ERROR: %s is not a valid input file for ionstats reduce\n", input_jsons[0].c_str());
    return 1;
  }
  string format_name = first_input_json["meta"].get("format_name","").asString();

  if (format_name == "ionstats_basecaller")
    return IonstatsBasecallerReduce(output_json_filename, input_jsons);
  if (format_name == "ionstats_tf")
    return IonstatsTestFragmentsReduce(output_json_filename, input_jsons);
  if (format_name == "ionstats_alignment")
    return IonstatsAlignmentReduce(output_json_filename, input_jsons);

  fprintf(stderr, "[ionstats] ERROR: %s is not a valid input file for ionstats reduce\n", input_jsons[0].c_str());
  return 1;
}

int main(int argc, const char *argv[]) {
  OptArgs opts;
  string position_file;
  string h5file_in;
  string source;
  string h5file_out;
  string destination;
  string positions_file;
  bool help;
  string flowlimit_arg;
  unsigned int flowlimit;
  vector<string>otherArgs;

  DumpStartingStateOfExtractWells (argc,argv);

  opts.ParseCmdLine(argc, argv);
  opts.GetOption(h5file_in, "", 'i', "input");
  opts.GetOption(source, "", 's', "source");
  opts.GetOption(h5file_out, "", 'o', "output");
  opts.GetOption(destination, "", 'd', "destination");
  opts.GetOption(flowlimit_arg, "", 'f', "flowlimit");
  opts.GetOption(positions_file, "", 'p', "positions");
  opts.GetOption(help, "false", 'h', "help");
  opts.GetLeftoverArguments(otherArgs);

  // input data processing
  string line;
  vector<size_t> row_val;
  vector<size_t> col_val;
  ifstream filestream;
  if ( ! positions_file.empty() )
    filestream.open(&positions_file.At(0));
  istream &input = ( filestream.is_open() ) ? filestream : cin;


		      
  while ( getline(input, line) )
  {
    int num = -1;
    vector<size_t> ints;
    istringstream ss(line);
    while ( ss >> num && ints.size() < 2 ) {
      if (num < 0) {
	fprintf(stderr, "Found negative integer %d\n", num);
	exit(-1);
      }
      else
	ints.push_back((size_t)num);
    }
    if (ints.size() != 2) {
      fprintf(stderr, "Found %d integers in %s, expected 2\n", (int)ints.size(), &line[0]);
      continue;
    }
    row_val.push_back(ints.at(0));
    col_val.push_back(ints.at(1));
  }
  if (row_val.size() == 0 ) {
      fprintf(stdout, "No positions to extract, check input\n");
      exit(0);
  }    
  vector<size_t>input_positions(row_val.size(), 0);

  int numCPU = (int)sysconf( _SC_NPROCESSORS_ONLN );
  int numThreads = MAXTHREADS < numCPU ? MAXTHREADS : numCPU;
  fprintf(stdout, "Using %d threads of %d cores\n", numThreads, numCPU);

  if (source.empty())
    source = source + SIGNAL_IN;
  H5ReplayReader reader = H5ReplayReader(h5file_in, &source[0]);
  if ( h5file_out.empty() )
    h5file_out = h5file_out + H5FILE_OUT;
  if ( destination.empty() )
    destination = destination + SIGNAL_OUT;

  reader.Open();
  int rank = reader.GetRank();
  vector<hsize_t>dims(rank);
  vector<hsize_t>chunks(rank);
  reader.GetDims(dims);
  reader.GetChunkSize(chunks);
  reader.Close();

  // convert input row, col positions to indices
  for (hsize_t i=0; i<input_positions.size(); i++)
    input_positions.At(i) = RowColToIndex(row_val.At(i), col_val.At(i), dims.At(0), dims.At(1));
  sort(input_positions.begin(), input_positions.end());

  fprintf(stdout, "Opened for read %s:%s with rank %d, row x col x flow dims=[ ", &h5file_in[0], &source[0], rank);
  for (int i=0; i<rank; i++)
    fprintf(stdout, "%d ", (int)dims.At(i));
  fprintf(stdout, "], chunksize=[ ");
  for (int i=0; i<rank; i++)
    fprintf(stdout, "%d ", (int)chunks.At(i));
  fprintf(stdout, "]\n");

  
  H5ReplayRecorder recorder = H5ReplayRecorder(h5file_out, &destination[0],reader.GetType(),2);
  recorder.CreateFile();


//.........这里部分代码省略.........

int main(int argc, const char *argv[])
{
    OptArgs opts;
    opts.ParseCmdLine(argc, argv);
    bool help, combineSffs;
    string sffFile;
    string bamFile;
    vector<string> infiles;
    opts.GetOption(help,"false", 'h', "help");
    opts.GetOption(combineSffs,"false", 'c', "combine-sffs");
    opts.GetOption(bamFile,"",'o',"out-filename");
    opts.GetLeftoverArguments(infiles);

    if(help || infiles.empty())
    {
        usage();
    }

	if((!combineSffs) && infiles.size() > 1)
	{
        cerr << "sff2bam ERROR: if you want to combine all sff files into a single bam file, please use option -c true." << endl;
        usage();
	}

    sffFile= infiles.front();

    if(bamFile.length() < 1)
    {
        bamFile = sffFile.substr(0, sffFile.length() - 3);
        bamFile += "bam";
    }

    sff_file_t* sff_file = sff_fopen(sffFile.c_str(), "r", NULL, NULL);
    if(!sff_file)
    {
        cerr << "sff2bam ERROR: fail to open " << sffFile << endl;
        exit(1);
    }

	// All sff files must have the same flow and key
	if(combineSffs && infiles.size() > 1)
	{
        for(size_t n = 1; n < infiles.size(); ++n)
		{
			sff_file_t* sff_file2 = sff_fopen(infiles[n].c_str(), "r", NULL, NULL);
			if(!sff_file2)
			{
				sff_fclose(sff_file);
				cerr << "sff2bam ERROR: fail to open " << infiles[n] << endl;
				exit(1);
			}

			if(strcmp(sff_file2->header->flow->s, sff_file->header->flow->s) != 0 ||
				strcmp(sff_file2->header->key->s, sff_file->header->key->s) != 0)
			{
				sff_fclose(sff_file);
				sff_fclose(sff_file2);
				cerr << "sff2bam ERROR: " << sffFile << " and " << infiles[n] << " have different flows or keys." << endl;
				exit(1);
			}

			sff_fclose(sff_file2);
		}
	}

    sff_t* sff = NULL;
    // Open 1st read for read group name
    sff = sff_read(sff_file);
    if(!sff)
    {
        sff_fclose(sff_file);
        cerr << "sff2bam ERROR: fail to read " << sffFile << endl;
        exit(1);
    }

    // Set up BAM header
    SamHeader sam_header;
    sam_header.Version = "1.4";
    sam_header.SortOrder = "unsorted";

    SamProgram sam_program("sff2bam");
    sam_program.Name = "sff2bam";
    sam_program.Version = SFF2BAM_VERSION;
    sam_program.CommandLine = "sff2bam";
    sam_header.Programs.Add(sam_program);

    string rgname = sff->rheader->name->s;
    int index = rgname.find(":");
    rgname = rgname.substr(0, index);

    SamReadGroup read_group(rgname);
    read_group.FlowOrder = sff->gheader->flow->s;
    read_group.KeySequence = sff->gheader->key->s;

    sam_header.ReadGroups.Add(read_group);

    RefVector refvec;
    BamWriter bamWriter;
    bamWriter.SetCompressionMode(BamWriter::Compressed);

//.........这里部分代码省略.........

int main(int argc, const char *argv[]) {
  OptArgs opts;  
  string h5file;
  string source;
  string destination;
  vector<string> infiles;
  bool help;
  string flowlimit_arg;
  unsigned int flowlimit;

  DumpStartingStateOfNormWells (argc,argv);

  opts.ParseCmdLine(argc, argv);
  opts.GetOption(h5file, "", '-', "h5file");
  opts.GetOption(source, "", 's', "source");
  opts.GetOption(destination, "", 'd', "destination");
  opts.GetOption(flowlimit_arg, "", 'f', "flowlimit");
  opts.GetOption(help, "false", 'h', "help");
  opts.GetLeftoverArguments(infiles);
  if(help || infiles.empty() || (infiles.size() > 1) ) {
    usage();
  }
  h5file = infiles.front();

  int numCPU = (int)sysconf( _SC_NPROCESSORS_ONLN );
  int numThreads = MAXTHREADS < numCPU ? MAXTHREADS : numCPU;
  fprintf(stdout, "Using %d threads of %d cores\n", numThreads, numCPU);

  if (source.empty())
    source = source + SIGNAL_IN;
  H5ReplayReader reader = H5ReplayReader(h5file, &source[0]);
  if ( destination.empty() )
    destination = destination + SIGNAL_OUT;

  H5ReplayRecorder recorder = (source.compare(destination)==0)
    ? H5ReplayRecorder(h5file, &destination[0])
    : H5ReplayRecorder(h5file, &destination[0],reader.GetType(),reader.GetRank());

  reader.Open();
  int rank = reader.GetRank();
  vector<hsize_t>dims(rank,0);
  vector<hsize_t>chunks(rank,0);
  reader.GetDims(dims);
  reader.GetChunkSize(chunks);
  reader.Close();

  fprintf(stdout, "Opening for read %s:%s with rank %d, row x col x flow dims=[ ", &h5file[0], &source[0], rank);
  for (int i=0; i<rank; i++)
    fprintf(stdout, "%d ", (int)dims[i]);
  fprintf(stdout, "], chunksize=[ ");
  for (int i=0; i<rank; i++)
    fprintf(stdout, "%d ", (int)chunks[i]);
  fprintf(stdout, "]\n");

  if (flowlimit_arg.empty())
    flowlimit = dims[2];
  else
    flowlimit = atoi(flowlimit_arg.c_str());

  flowlimit = (flowlimit < dims[2]) ? flowlimit : dims[2];
  fprintf(stdout, "Using %u flows\n", flowlimit);

  // hard code region size to be at least 100x100
  chunks[0] = (chunks[0] < 100) ? 100 : chunks[0];
  chunks[1] = (chunks[1] < 100) ? 100 : chunks[1];

  recorder.CreateDataset(chunks);
  
  int max_threads_ever = (dims[0]/chunks[0] +1)*(dims[1]/chunks[1] +1);
  thread_flags.resize (max_threads_ever, 0);
  // fprintf(stdout, "max_threads_ever = %d\n", max_threads_ever);
  unsigned int thread_id = 0;
  vector<compute_norm_args> my_args( max_threads_ever );
  
  // layout is rows x cols x flows
  for (hsize_t row=0; row<dims[0]; ) {
    for (hsize_t col=0; col<dims[1]; ) {
      pthread_t thread;
      int thread_status;

      assert( thread_id < thread_flags.size() );
      my_args.at(thread_id).row = row;
      my_args.at(thread_id).col = col;
      my_args.at(thread_id).chunks = &chunks;
      my_args.at(thread_id).dims = &dims;
      my_args.at(thread_id).h5file = &h5file;
      my_args.at(thread_id).source = &source;
      my_args.at(thread_id).destination = &destination;
      my_args.at(thread_id).thread_id = thread_id;
      my_args.at(thread_id).flowlimit = flowlimit;

      fprintf(stdout, "creating thread %d from row=%d (max %d), column=%d (max %d)\n", thread_id, (int)row, (int)dims[0], (int)col, (int)dims[1]);
      while (accumulate(thread_flags.begin(), thread_flags.end(), 0) > numThreads) {
	// only have to be approximate, don't worry about races
	// fprintf(stdout, "Sleeping ...\n");
	sleep(1);
      }
      thread_flags[thread_id] = 1;
      thread_status = pthread_create(&thread, NULL, compute_norm, (void *)&my_args[thread_id]);
      // compute_norm((void *)&my_args[thread_id]);
//.........这里部分代码省略.........