global-1/ufasta/extract_cmdline.hpp

/***** This code was generated by Yaggo. Do not edit ******/

#ifndef __EXTRACT_CMDLINE_HPP__
#define __EXTRACT_CMDLINE_HPP__

#include <stdint.h>
#include <unistd.h>
#include <stdlib.h>
#include <getopt.h>
#include <errno.h>
#include <string.h>
#include <stdexcept>
#include <string>
#include <limits>
#include <vector>
#include <iostream>
#include <sstream>
#include <memory>

class extract_cmdline {
 // Boiler plate stuff. Conversion from string to other formats
  static bool adjust_double_si_suffix(double &res, const char *suffix) {
    if(*suffix == '\0')
      return true;
    if(*(suffix + 1) != '\0')
      return false;

    switch(*suffix) {
    case 'a': res *= 1e-18; break;
    case 'f': res *= 1e-15; break;
    case 'p': res *= 1e-12; break;
    case 'n': res *= 1e-9;  break;
    case 'u': res *= 1e-6;  break;
    case 'm': res *= 1e-3;  break;
    case 'k': res *= 1e3;   break;
    case 'M': res *= 1e6;   break;
    case 'G': res *= 1e9;   break;
    case 'T': res *= 1e12;  break;
    case 'P': res *= 1e15;  break;
    case 'E': res *= 1e18;  break;
    default: return false;
    }
    return true;
  }

  static double conv_double(const char *str, ::std::string &err, bool si_suffix) {
    char *endptr = 0;
    errno = 0;
    double res = strtod(str, &endptr);
    if(errno) {
      err.assign(strerror(errno));
      return (double)0.0;
    }
    bool invalid =
      si_suffix ? !adjust_double_si_suffix(res, endptr) : *endptr != '\0';
    if(invalid) {
      err.assign("Invalid character");
      return (double)0.0;
    }
    return res;
  }

  static int conv_enum(const char* str, ::std::string& err, const char* const strs[]) {
    int res = 0;
    for(const char* const* cstr = strs; *cstr; ++cstr, ++res)
      if(!strcmp(*cstr, str))
        return res;
    err += "Invalid constant '";
    err += str;
    err += "'. Expected one of { ";
    for(const char* const* cstr = strs; *cstr; ++cstr) {
      if(cstr != strs)
        err += ", ";
      err += *cstr;
    }
    err += " }";
    return -1;
  }

  template<typename T>
  static bool adjust_int_si_suffix(T &res, const char *suffix) {
    if(*suffix == '\0')
      return true;
    if(*(suffix + 1) != '\0')
      return false;

    switch(*suffix) {
    case 'k': res *= (T)1000; break;
    case 'M': res *= (T)1000000; break;
    case 'G': res *= (T)1000000000; break;
    case 'T': res *= (T)1000000000000; break;
    case 'P': res *= (T)1000000000000000; break;
    case 'E': res *= (T)1000000000000000000; break;
    default: return false;
    }
    return true;
  }

  template<typename T>
  static T conv_int(const char *str, ::std::string &err, bool si_suffix) {
    char *endptr = 0;
    errno = 0;
    long long int res = strtoll(str, &endptr, 0);
    if(errno) {
      err.assign(strerror(errno));
      return (T)0;
    }
    bool invalid =
      si_suffix ? !adjust_int_si_suffix(res, endptr) : *endptr != '\0';
    if(invalid) {
      err.assign("Invalid character");
      return (T)0;
    }
    if(res > ::std::numeric_limits<T>::max() ||
       res < ::std::numeric_limits<T>::min()) {
      err.assign("Value out of range");
      return (T)0;
    }
    return (T)res;
  }

  template<typename T>
  static T conv_uint(const char *str, ::std::string &err, bool si_suffix) {
    char *endptr = 0;
    errno = 0;
    while(isspace(*str)) { ++str; }
    if(*str == '-') {
      err.assign("Negative value");
      return (T)0;
    }
    unsigned long long int res = strtoull(str, &endptr, 0);
    if(errno) {
      err.assign(strerror(errno));
      return (T)0;
    }
    bool invalid =
      si_suffix ? !adjust_int_si_suffix(res, endptr) : *endptr != '\0';
    if(invalid) {
      err.assign("Invalid character");
      return (T)0;
    }
    if(res > ::std::numeric_limits<T>::max()) {
      err.assign("Value out of range");
      return (T)0;
    }
    return (T)res;
  }

  template<typename T>
  static ::std::string vec_str(const std::vector<T> &vec) {
    ::std::ostringstream os;
    for(typename ::std::vector<T>::const_iterator it = vec.begin();
        it != vec.end(); ++it) {
      if(it != vec.begin())
        os << ",";
      os << *it;
    }
    return os.str();
  }

  class string : public ::std::string {
  public:
    string() : ::std::string() {}
    explicit string(const ::std::string &s) : std::string(s) {}
    explicit string(const char *s) : ::std::string(s) {}
    int as_enum(const char* const strs[]) {
      ::std::string err;
      int res = conv_enum((const char*)this->c_str(), err, strs);
      if(!err.empty())
        throw ::std::runtime_error(err);
      return res;
    }


    uint32_t as_uint32_suffix() const { return as_uint32(true); }
    uint32_t as_uint32(bool si_suffix = false) const {
      ::std::string err;
      uint32_t res = conv_uint<uint32_t>((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to uint32_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
    uint64_t as_uint64_suffix() const { return as_uint64(true); }
    uint64_t as_uint64(bool si_suffix = false) const {
      ::std::string err;
      uint64_t res = conv_uint<uint64_t>((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to uint64_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
    int32_t as_int32_suffix() const { return as_int32(true); }
    int32_t as_int32(bool si_suffix = false) const {
      ::std::string err;
      int32_t res = conv_int<int32_t>((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to int32_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
    int64_t as_int64_suffix() const { return as_int64(true); }
    int64_t as_int64(bool si_suffix = false) const {
      ::std::string err;
      int64_t res = conv_int<int64_t>((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to int64_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
    int as_int_suffix() const { return as_int(true); }
    int as_int(bool si_suffix = false) const {
      ::std::string err;
      int res = conv_int<int>((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to int_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
    long as_long_suffix() const { return as_long(true); }
    long as_long(bool si_suffix = false) const {
      ::std::string err;
      long res = conv_int<long>((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to long_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
    double as_double_suffix() const { return as_double(true); }
    double as_double(bool si_suffix = false) const {
      ::std::string err;
      double res = conv_double((const char*)this->c_str(), err, si_suffix);
      if(!err.empty()) {
        ::std::string msg("Invalid conversion of '");
        msg += *this;
        msg += "' to double_t: ";
        msg += err;
        throw ::std::runtime_error(msg);
      }
      return res;
    }
  };

public:
  bool                           invert_match_flag;
  ::std::vector<string>          name_arg;
  typedef ::std::vector<string>::iterator name_arg_it;
  typedef ::std::vector<string>::const_iterator name_arg_const_it;
  bool                           name_given;
  ::std::vector<const char *>    name_file_arg;
  typedef ::std::vector<const char *>::iterator name_file_arg_it;
  typedef ::std::vector<const char *>::const_iterator name_file_arg_const_it;
  bool                           name_file_given;
  double                         probabilistic_arg;
  bool                           probabilistic_given;
  uint64_t                       max_count_arg;
  bool                           max_count_given;
  uint64_t                       start_arg;
  bool                           start_given;
  uint64_t                       end_arg;
  bool                           end_given;
  ::std::vector<const char *>    file_arg;
  typedef ::std::vector<const char *>::iterator file_arg_it;
  typedef ::std::vector<const char *>::const_iterator file_arg_const_it;

  enum {
    START_OPT = 1000
  };

  extract_cmdline() :
    invert_match_flag(false),
    name_arg(), name_given(false),
    name_file_arg(), name_file_given(false),
    probabilistic_arg(0.0), probabilistic_given(false),
    max_count_arg(0), max_count_given(false),
    start_arg(0), start_given(false),
    end_arg(0), end_given(false),
    file_arg()
  { }

  extract_cmdline(int argc, char* argv[]) :
    invert_match_flag(false),
    name_arg(), name_given(false),
    name_file_arg(), name_file_given(false),
    probabilistic_arg(0.0), probabilistic_given(false),
    max_count_arg(0), max_count_given(false),
    start_arg(0), start_given(false),
    end_arg(0), end_given(false),
    file_arg()
  { parse(argc, argv); }

  void parse(int argc, char* argv[]) {
    static struct option long_options[] = {
      {"invert-match", 0, 0, 'v'},
      {"name", 1, 0, 'n'},
      {"name-file", 1, 0, 'f'},
      {"probabilistic", 1, 0, 'p'},
      {"max-count", 1, 0, 'm'},
      {"start", 1, 0, 's'},
      {"end", 1, 0, 'e'},
      {"help", 0, 0, 'h'},
      {"usage", 0, 0, 'U'},
      {"version", 0, 0, 'V'},
      {0, 0, 0, 0}
    };
    static const char *short_options = "hVUvn:f:p:m:s:e:";

    ::std::string err;
#define CHECK_ERR(type,val,which) if(!err.empty()) { ::std::cerr << "Invalid " #type " '" << val << "' for [" which "]: " << err << "\n"; exit(1); }
    while(true) {
      int index = -1;
      int c = getopt_long(argc, argv, short_options, long_options, &index);
      if(c == -1) break;
      switch(c) {
      case ':':
        ::std::cerr << "Missing required argument for "
                  << (index == -1 ? ::std::string(1, (char)optopt) : std::string(long_options[index].name))
                  << ::std::endl;
        exit(1);
      case 'h':
        ::std::cout << usage() << "\n\n" << help() << std::endl;
        exit(0);
      case 'U':
        ::std::cout << usage() << "\nUse --help for more information." << std::endl;
        exit(0);
      case 'V':
        print_version();
        exit(0);
      case '?':
        ::std::cerr << "Use --usage or --help for some help\n";
        exit(1);
      case 'v':
        invert_match_flag = true;
        break;
      case 'n':
        name_given = true;
        name_arg.push_back(string(optarg));
        break;
      case 'f':
        name_file_given = true;
        name_file_arg.push_back(optarg);
        break;
      case 'p':
        probabilistic_given = true;
        probabilistic_arg = conv_double((const char*)optarg, err, false);
        CHECK_ERR(double_t, optarg, "-p, --probabilistic=PROBA")
        break;
      case 'm':
        max_count_given = true;
        max_count_arg = conv_uint<uint64_t>((const char*)optarg, err, false);
        CHECK_ERR(uint64_t, optarg, "-m, --max-count=NUM")
        break;
      case 's':
        start_given = true;
        start_arg = conv_uint<uint64_t>((const char*)optarg, err, false);
        CHECK_ERR(uint64_t, optarg, "-s, --start=NUM")
        break;
      case 'e':
        end_given = true;
        end_arg = conv_uint<uint64_t>((const char*)optarg, err, false);
        CHECK_ERR(uint64_t, optarg, "-e, --end=NUM")
        break;
      }
    }

    // Parse arguments
    if(argc - optind < 0)
      error("Requires at least 0 argument.");
    for( ; optind < argc; ++optind) {
      file_arg.push_back(argv[optind]);
    }
  }
  static const char * usage() { return "Usage: extract_cmdline [options] file:string+"; }
  class error {
    int code_;
    std::ostringstream msg_;

    // Select the correct version (GNU or XSI) version of
    // strerror_r. strerror_ behaves like the GNU version of strerror_r,
    // regardless of which version is provided by the system.
    static const char* strerror__(char* buf, int res) {
      return res != -1 ? buf : "Invalid error";
    }
    static const char* strerror__(char* buf, char* res) {
      return res;
    }
    static const char* strerror_(int err, char* buf, size_t buflen) {
      return strerror__(buf, strerror_r(err, buf, buflen));
    }
    struct no_t { };

  public:
    static no_t no;
    error(int code = EXIT_FAILURE) : code_(code) { }
    explicit error(const char* msg, int code = EXIT_FAILURE) : code_(code)
      { msg_ << msg; }
    error(const std::string& msg, int code = EXIT_FAILURE) : code_(code)
      { msg_ << msg; }
    error& operator<<(no_t) {
      char buf[1024];
      msg_ << ": " << strerror_(errno, buf, sizeof(buf));
      return *this;
    }
    template<typename T>
    error& operator<<(const T& x) { msg_ << x; return (*this); }
    ~error() {
      ::std::cerr << "Error: " << msg_.str() << "\n"
                  << usage() << "\n"
                  << "Use --help for more information"
                  << ::std::endl;
      exit(code_);
    }
  };
  static const char * help() { return
    "Match a header and output the content.\n\n"
    "Options (default value in (), *required):\n"
    " -v, --invert-match                       Invert the sense of matching, to select non-matching headers (false)\n"
    " -n, --name=NAME                          Extract read with NAME, exact match\n"
    " -f, --name-file=path                     File of read names to extract\n"
    " -p, --probabilistic=PROBA                Select sequences with probability PROBA\n"
    " -m, --max-count=NUM                      Stop reading after NUM matching headers\n"
    " -s, --start=NUM                          Output content starting at byte NUM, 0-based\n"
    " -e, --end=NUM                            Output content up to byte NUM\n"
    " -U, --usage                              Usage\n"
    " -h, --help                               This message\n"
    " -V, --version                            Version";
  }
  static const char* hidden() { return ""; }
  void print_version(::std::ostream &os = std::cout) const {
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.0.0"
#endif
    os << PACKAGE_VERSION << "\n";
  }
  void dump(::std::ostream &os = std::cout) {
    os << "invert_match_flag:" << invert_match_flag << "\n";
    os << "name_given:" << name_given << " name_arg:" << vec_str(name_arg) << "\n";
    os << "name_file_given:" << name_file_given << " name_file_arg:" << vec_str(name_file_arg) << "\n";
    os << "probabilistic_given:" << probabilistic_given << " probabilistic_arg:" << probabilistic_arg << "\n";
    os << "max_count_given:" << max_count_given << " max_count_arg:" << max_count_arg << "\n";
    os << "start_given:" << start_given << " start_arg:" << start_arg << "\n";
    os << "end_given:" << end_given << " end_arg:" << end_arg << "\n";
    os << "file_arg:" << vec_str(file_arg) << "\n";
  }
};
#endif // __EXTRACT_CMDLINE_HPP__"