/***** This code was generated by Yaggo. Do not edit ******/
/* This file is part of Jellyfish.
Jellyfish is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Jellyfish is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Jellyfish. If not, see .
*/
#ifndef __HISTO_MAIN_CMDLINE_HPP__
#define __HISTO_MAIN_CMDLINE_HPP__
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
class histo_main_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
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
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::max() ||
res < ::std::numeric_limits::min()) {
err.assign("Value out of range");
return (T)0;
}
return (T)res;
}
template
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::max()) {
err.assign("Value out of range");
return (T)0;
}
return (T)res;
}
template
static ::std::string vec_str(const std::vector &vec) {
::std::ostringstream os;
for(typename ::std::vector::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((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((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((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((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((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((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:
uint64_t low_arg;
bool low_given;
uint64_t high_arg;
bool high_given;
uint64_t increment_arg;
bool increment_given;
uint32_t threads_arg;
bool threads_given;
bool full_flag;
const char * output_arg;
bool output_given;
uint64_t buffer_size_arg;
bool buffer_size_given;
bool verbose_flag;
const char * db_arg;
enum {
START_OPT = 1000,
FULL_HELP_OPT,
HELP_OPT
};
histo_main_cmdline() :
low_arg((uint64_t)1), low_given(false),
high_arg((uint64_t)10000), high_given(false),
increment_arg((uint64_t)1), increment_given(false),
threads_arg((uint32_t)1), threads_given(false),
full_flag(false),
output_arg(""), output_given(false),
buffer_size_arg((uint64_t)10000000), buffer_size_given(false),
verbose_flag(false),
db_arg("")
{ }
histo_main_cmdline(int argc, char* argv[]) :
low_arg((uint64_t)1), low_given(false),
high_arg((uint64_t)10000), high_given(false),
increment_arg((uint64_t)1), increment_given(false),
threads_arg((uint32_t)1), threads_given(false),
full_flag(false),
output_arg(""), output_given(false),
buffer_size_arg((uint64_t)10000000), buffer_size_given(false),
verbose_flag(false),
db_arg("")
{ parse(argc, argv); }
void parse(int argc, char* argv[]) {
static struct option long_options[] = {
{"low", 1, 0, 'l'},
{"high", 1, 0, 'h'},
{"increment", 1, 0, 'i'},
{"threads", 1, 0, 't'},
{"full", 0, 0, 'f'},
{"output", 1, 0, 'o'},
{"buffer-size", 1, 0, 's'},
{"verbose", 0, 0, 'v'},
{"help", 0, 0, HELP_OPT},
{"full-help", 0, 0, FULL_HELP_OPT},
{"usage", 0, 0, 'U'},
{"version", 0, 0, 'V'},
{0, 0, 0, 0}
};
static const char *short_options = "VUl:h:i:t:fo:s:v";
::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 HELP_OPT:
::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 FULL_HELP_OPT:
::std::cout << usage() << "\n\n" << help() << "\n\n" << hidden() << std::flush;
exit(0);
case 'l':
low_given = true;
low_arg = conv_uint((const char*)optarg, err, false);
CHECK_ERR(uint64_t, optarg, "-l, --low=uint64")
break;
case 'h':
high_given = true;
high_arg = conv_uint((const char*)optarg, err, false);
CHECK_ERR(uint64_t, optarg, "-h, --high=uint64")
break;
case 'i':
increment_given = true;
increment_arg = conv_uint((const char*)optarg, err, false);
CHECK_ERR(uint64_t, optarg, "-i, --increment=uint64")
break;
case 't':
threads_given = true;
threads_arg = conv_uint((const char*)optarg, err, false);
CHECK_ERR(uint32_t, optarg, "-t, --threads=uint32")
break;
case 'f':
full_flag = true;
break;
case 'o':
output_given = true;
output_arg = optarg;
break;
case 's':
buffer_size_given = true;
buffer_size_arg = conv_uint((const char*)optarg, err, true);
CHECK_ERR(uint64_t, optarg, "-s, --buffer-size=Buffer length")
break;
case 'v':
verbose_flag = true;
break;
}
}
// Parse arguments
if(argc - optind != 1)
error("Requires exactly 1 argument.");
db_arg = argv[optind];
++optind;
}
static const char * usage() { return "Usage: jellyfish histo [options] db:path"; }
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
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
"Create an histogram of k-mer occurrences\n\nCreate an histogram with the number of k-mers having a given\n" \
"count. In bucket 'i' are tallied the k-mers which have a count 'c'\n" \
"satisfying 'low+i*inc <= c < low+(i+1)*inc'. Buckets in the output are\n" \
"labeled by the low end point (low+i*inc).\n" \
"\n" \
"The last bucket in the output behaves as a catchall: it tallies all\n" \
"k-mers with a count greater or equal to the low end point of this\n" \
"bucket.\n\n"
"Options (default value in (), *required):\n"
" -l, --low=uint64 Low count value of histogram (1)\n"
" -h, --high=uint64 High count value of histogram (10000)\n"
" -i, --increment=uint64 Increment value for buckets (1)\n"
" -t, --threads=uint32 Number of threads (1)\n"
" -f, --full Full histo. Don't skip count 0. (false)\n"
" -o, --output=string Output file\n"
" -v, --verbose Output information (false)\n"
" -U, --usage Usage\n"
" --help This message\n"
" --full-help Detailed help\n"
" -V, --version Version";
}
static const char* hidden() { return
"Hidden options:\n"
" -s, --buffer-size=Buffer length Length in bytes of input buffer (10000000)\n"
"";
}
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 << "low_given:" << low_given << " low_arg:" << low_arg << "\n";
os << "high_given:" << high_given << " high_arg:" << high_arg << "\n";
os << "increment_given:" << increment_given << " increment_arg:" << increment_arg << "\n";
os << "threads_given:" << threads_given << " threads_arg:" << threads_arg << "\n";
os << "full_flag:" << full_flag << "\n";
os << "output_given:" << output_given << " output_arg:" << output_arg << "\n";
os << "buffer_size_given:" << buffer_size_given << " buffer_size_arg:" << buffer_size_arg << "\n";
os << "verbose_flag:" << verbose_flag << "\n";
os << "db_arg:" << db_arg << "\n";
}
};
#endif // __HISTO_MAIN_CMDLINE_HPP__"