squeakr.cc
/*
* ============================================================================
*
* Authors: Prashant Pandey <ppandey@cs.stonybrook.edu>
* Rob Johnson <robj@vmware.com>
* Rob Patro (rob.patro@cs.stonybrook.edu)
*
* ============================================================================
*/
#include <iostream>
#include <string>
#include <vector>
#include <cassert>
#include <exception>
#include "ProgOpts.h"
#include "clipp.h"
#include "SqueakrFS.h"
template <typename T>
void explore_options_verbose(T& res) {
if(res.any_error()) { std::cerr << "error\n"; }
//aggregated errors
if(res.unmapped_args_count()) { std::cerr << "error unmapped args count\n"; /* ... */ }
if(res.any_bad_repeat()) { std::cerr << "error bad repeat \n"; /* ... */ }
if(res.any_blocked()) { std::cerr << "error blocked \n"; /* ... */ }
if(res.any_conflict()) { std::cerr << "error conflict\n"; /* ... */ }
for(const auto& m : res.missing()) {
std::cerr << "missing " << m.param() << " after index " << m.after_index() << '\n';
}
//per-argument mapping
for(const auto& m : res) {
std::cerr << m.index() << ": " << m.arg() << " -> " << m.param();
std::cerr << " repeat #" << m.repeat();
if(m.blocked()) std::cerr << " blocked";
if(m.conflict()) std::cerr << " conflict";
std::cerr<< '\n';
}
}
int query_main (QueryOpts& opt);
int count_main (CountOpts& opt);
int inner_prod_main (InnerProdOpts& opt);
int list_main (ListOpts& opt);
int info_main (InfoOpts& opt);
/*
* === FUNCTION =============================================================
* Name: main
* Description:
* ============================================================================
*/
int main ( int argc, char *argv[] ) {
using namespace clipp;
enum class mode {count, query, inner_prod, list, info, help};
mode selected = mode::help;
auto console = spdlog::stdout_color_mt("squeakr_console");
CountOpts countopt;
QueryOpts queryopt;
InnerProdOpts innerprodopt;
ListOpts listopt;
InfoOpts infoopt;
countopt.console = console;
queryopt.console = console;
innerprodopt.console = console;
listopt.console = console;
infoopt.console = console;
auto ensure_file_exists = [](const std::string& s) -> bool {
bool exists = squeakr::fs::FileExists(s.c_str());
if (!exists) {
std::string e = "The required input file " + s + " does not seem to exist.";
throw std::runtime_error{e};
}
return true;
};
auto ensure_parent_dir_exists = [](const std::string& s) -> bool {
std::string parent_dir = squeakr::fs::GetDir(s);
bool exists = squeakr::fs::DirExists(parent_dir.c_str());
if (!exists) {
std::string e = "The required input directory " + parent_dir + " does not seem to exist.";
throw std::runtime_error{e};
}
return true;
};
auto enusure_size_is_specified = [](const CountOpts countopt) -> bool {
if (!countopt.setqbits && countopt.numthreads == 0) {
std::string e = "Size option is required if the thread count is greater than 1.";
throw std::runtime_error{e};
}
return true;
};
auto count_mode = (
command("count").set(selected, mode::count),
option("-e", "--exact").set(countopt.exact, 1) %
"squeakr-exact (default is Squeakr approximate)",
required("-k","--kmer") & value("k-size", countopt.ksize) %
"length of k-mers to count",
option("-c","--cutoff") & value("cutoff", countopt.cutoff) %
"only output k-mers with count greater than or equal to cutoff (default = 1)",
option("-n","--no-counts").set(countopt.contains_counts, 0) %
"only output k-mers and no counts (default = false)",
option("-s","--log-slots").set(countopt.setqbits, true) &
value("log-slots", countopt.qbits) % "log of number of slots in the CQF. (Size argument is only optional when numthreads is exactly 1.)",
option("-t","--threads") & value("num-threads",
countopt.numthreads) %
"number of threads to use to count (default = number of hardware threads)",
required("-o","--output-file") &
value(ensure_parent_dir_exists, "out-file",
countopt.output_file) %
"file in which output should be written",
values(ensure_file_exists, "files", countopt.filenames) % "list of files to be counted (supported files: fastq and compressed gzip or bzip2 fastq files)"
//option("-h", "--help") % "show help"
);
auto query_mode = (
command("query").set(selected, mode::query),
required("-f", "--squeakr-file") & value(ensure_file_exists, "squeakr-file",
queryopt.squeakr_file) % "input squeakr file",
required("-q","--query-file") & value(ensure_file_exists, "query-file",
queryopt.queryfile) % "input query file",
required("-o", "--output-file") &
value(ensure_parent_dir_exists, "output-file",
queryopt.output_file) % "output file"
//option("-h", "--help") % "show help"
);
auto inner_prod_mode = (
command("inner_prod").set(selected, mode::inner_prod),
value(ensure_file_exists, "first-input",
innerprodopt.squeakr_filea)
% "first input squeakr file",
value(ensure_file_exists, "second-input",
innerprodopt.squeakr_fileb)
% "second input squeakr file"
//option("-h", "--help") % "show help"
);
auto list_mode = (
command("list").set(selected, mode::list),
required("-f", "--squeakr-file-file") & value(ensure_file_exists, "squeakr-file",
listopt.squeakr_file) % "input squeakr file",
required("-o", "--output-file") &
value(ensure_parent_dir_exists, "output-file",
listopt.output_file) % "output file"
//option("-h", "--help") % "show help"
);
auto info_mode = (
command("info").set(selected, mode::info),
required("-f", "--squeakr-file-file") & value(ensure_file_exists, "squeakr-file",
infoopt.squeakr_file) % "input squeakr file"
//option("-h", "--help") % "show help"
);
auto cli = (
(count_mode | query_mode | inner_prod_mode | list_mode |
info_mode |
command("help").set(selected,mode::help) ),
option("-v", "--version").call([]{std::cout << "version 1.0\n\n";}).doc("show version")
);
assert(count_mode.flags_are_prefix_free());
assert(query_mode.flags_are_prefix_free());
assert(inner_prod_mode.flags_are_prefix_free());
assert(list_mode.flags_are_prefix_free());
assert(info_mode.flags_are_prefix_free());
decltype(parse(argc, argv, cli)) res;
try {
res = parse(argc, argv, cli);
} catch (std::exception& e) {
std::cout << "\n\nParsing command line failed with exception: " <<
e.what() << "\n";
std::cout << "\n\n";
std::cout << make_man_page(cli, "squeakr");
return 1;
}
if(res) {
switch(selected) {
case mode::count:
try {
enusure_size_is_specified(countopt);
} catch (std::exception& e) {
std::cout << "\n\nParsing command line failed with exception: " <<
e.what() << "\n";
std::cout << "\n\n";
std::cout << make_man_page(cli, "squeakr");
return 1;
}
count_main(countopt);
break;
case mode::query: query_main(queryopt); break;
case mode::inner_prod: inner_prod_main(innerprodopt); break;
case mode::list: list_main(listopt); break;
case mode::info: info_main(infoopt); break;
case mode::help: break;
}
} else {
auto b = res.begin();
auto e = res.end();
if (std::distance(b,e) > 0) {
if (b->arg() == "count") {
std::cout << make_man_page(count_mode, "squeakr");
} else if (b->arg() == "query") {
std::cout << make_man_page(query_mode, "squeakr");
} else if (b->arg() == "inner_prod") {
std::cout << make_man_page(inner_prod_mode, "squeakr");
} else if (b->arg() == "list") {
std::cout << make_man_page(list_mode, "squeakr");
} else if (b->arg() == "info") {
std::cout << make_man_page(info_mode, "squeakr");
} else {
std::cout << "There is no command \"" << b->arg() << "\"\n";
std::cout << usage_lines(cli, "squeakr") << '\n';
}
} else {
std::cout << usage_lines(cli, "squeakr") << '\n';
}
}
return 0;
}
