Config::Config(int argc, const char **argv)
{
Command_line_parser parser;
parser.add_command("makedb", "Build DIAMOND database from a FASTA file")
.add_command("blastp", "Align amino acid query sequences against a protein reference database")
.add_command("blastx", "Align DNA query sequences against a protein reference database")
.add_command("view", "View DIAMOND alignment archive (DAA) formatted file")
.add_command("help", "Produce help message")
.add_command("version", "Display version information")
.add_command("getseq", "")
.add_command("benchmark", "")
.add_command("random-seqs", "")
.add_command("compare", "");
Options_group general ("General options");
general.add()
("threads", 'p', "number of CPU threads", threads_)
("db", 'd', "database file", database)
("out", 'o', "output file", output_file)
("outfmt", 'f', "output format (tab/sam/xml/daa)", output_format)
("verbose", 'v', "verbose console output", verbose)
("log", 0, "enable debug log", debug_log)
("quiet", 0, "disable console output", quiet);
Options_group makedb("Makedb options");
makedb.add()
("in", 0, "input reference file in FASTA format", input_ref_file)
#ifdef EXTRA
("dbtype", po::value<string>(&program_options::db_type), "database type (nucl/prot)")
#endif
;
Options_group aligner("Aligner options");
aligner.add()
("query",'q', "input query file", query_file)
("max-target-seqs",'k', "maximum number of target sequences to report alignments for", max_alignments, uint64_t(25))
("top", 0, "report alignments within this percentage range of top alignment score (overrides --max-target-seqs)", toppercent, 100.0)
("compress", 0, "compression for output files (0=none, 1=gzip)", compression)
("evalue",'e', "maximum e-value to report alignments", max_evalue, 0.001)
("min-score", 0, "minimum bit score to report alignments (overrides e-value setting)", min_bit_score)
("id", 0, "minimum identity% to report an alignment", min_id)
("query-cover", 0, "minimum query cover% to report an alignment", query_cover)
("sensitive", 0, "enable sensitive mode (default: fast)", mode_sensitive)
("more-sensitive", 0, "enable more sensitive mode (default: fast)", mode_more_sensitive)
("block-size", 'b', "sequence block size in billions of letters (default=2.0)", chunk_size, 2.0)
("index-chunks",'c', "number of chunks for index processing", lowmem, 4u)
("tmpdir",'t', "directory for temporary files", tmpdir)
("gapopen", 0, "gap open penalty (default=11 for protein)", gap_open, -1)
("gapextend", 0, "gap extension penalty (default=1 for protein)", gap_extend, -1)
#ifdef EXTRA
("reward", po::value<int>(&program_options::reward)->default_value(2), "match reward score (blastn only)")
("penalty", po::value<int>(&program_options::penalty)->default_value(-3), "mismatch penalty score (blastn only)")
#endif
("matrix", 0, "score matrix for protein alignment", matrix, string("blosum62"))
("seg", 0, "enable SEG masking of queries (yes/no)", seg)
("salltitles", 0, "print full subject titles in output files", salltitles);
Options_group advanced("Advanced options");
advanced.add()
("run-len", 'l', "mask runs between stop codons shorter than this length", run_len)
("freq-sd", 0, "number of standard deviations for ignoring frequent seeds", freq_sd, 0.0)
("id2", 0, "minimum number of identities for stage 1 hit", min_identities)
("window", 'w', "window size for local hit search", window)
("xdrop", 'x', "xdrop for ungapped alignment", xdrop, 20)
("gapped-xdrop", 'X', "xdrop for gapped alignment in bits", gapped_xdrop, 20)
("ungapped-score", 0, "minimum raw alignment score to continue local extension", min_ungapped_raw_score)
("hit-band", 0, "band for hit verification", hit_band)
("hit-score", 0, "minimum score to keep a tentative alignment", min_hit_score)
("band", 0, "band for dynamic programming computation", padding)
("shapes", 's', "number of seed shapes (0 = all available)", shapes)
("index-mode", 0, "index mode (0=4x12, 1=16x9)", index_mode)
("fetch-size", 0, "trace point fetch size", fetch_size, 4096u)
("rank-factor", 0, "include subjects within this range of max-target-seqs", rank_factor, 2.0)
("rank-ratio", 0, "include subjects within this ratio of last hit", rank_ratio, 0.35)
("single-domain", 0, "Discard secondary domains within one target sequence", single_domain)
("dbsize", 0, "effective database size (in letters)", db_size)
("no-auto-append", 0, "disable auto appending of DAA and DMND file extensions", no_auto_append)
("target-fetch-size", 0, "", target_fetch_size, 4u);
Options_group view_options("View options");
view_options.add()
("daa", 'a', "DIAMOND alignment archive (DAA) file", daa_file)
("forwardonly", 0, "only show alignments of forward strand", forwardonly);
Options_group hidden_options("");
hidden_options.add()
("extend-all", 0, "extend all seed hits", extend_all)
("local-align", 0, "Local alignment algorithm", local_align_mode, 0u)
("slow-search", 0, "", slow_search)
("seq", 0, "", seq_no)
("ht", 0, "", ht_mode)
("old-freq", 0, "", old_freq)
("qp", 0, "", query_parallel)
("match1", 0, "", match_file1)
("match2", 0, "", match_file2)
("max-hits", 'C', "maximum number of hits to consider for one seed", hit_cap)
("seed-freq", 0, "maximum seed frequency", max_seed_freq, -15.0);
parser.add(general).add(makedb).add(aligner).add(advanced).add(view_options).add(hidden_options);
parser.store(argc, argv, command);
switch (command) {
case Config::makedb:
if (input_ref_file == "")
throw std::runtime_error("Missing parameter: input file (--in)");
if (database == "")
throw std::runtime_error("Missing parameter: database file (--db/-d)");
if (chunk_size != 2.0)
throw std::runtime_error("Invalid option: --block-size/-b. Block size is set for the alignment commands.");
break;
case Config::blastp:
case Config::blastx:
if (query_file == "")
throw std::runtime_error("Missing parameter: query file (--query/-q)");
if (database == "")
throw std::runtime_error("Missing parameter: database file (--db/-d)");
if (daa_file.length() > 0) {
if (output_file.length() > 0)
throw std::runtime_error("Options --daa and --out cannot be used together.");
if (output_format.length() > 0 && output_format != "daa")
throw std::runtime_error("Invalid parameter: --daa/-a. Output file is specified with the --out/-o parameter.");
output_file = daa_file;
}
if (daa_file.length() > 0 || output_format == "daa") {
if (compression != 0)
throw std::runtime_error("Compression is not supported for DAA format.");
if (!no_auto_append)
auto_append_extension(output_file, ".daa");
}
break;
case Config::view:
if (daa_file == "")
throw std::runtime_error("Missing parameter: DAA file (--daa/-a)");
default:
;
}
if (hit_cap != 0)
throw std::runtime_error("Deprecated parameter: --max-hits/-C.");
if (debug_log)
verbosity = 3;
else if (quiet)
verbosity = 0;
else if (verbose)
verbosity = 2;
else if (((command == Config::view || command == blastx || command == blastp) && output_file == "")
|| command == Config::version)
verbosity = 0;
else
verbosity = 1;
switch (verbosity) {
case 0:
message_stream = Message_stream(false);
break;
case 3:
log_stream = Message_stream();
case 2:
verbose_stream = Message_stream();
default:
;
}
if (!no_auto_append) {
auto_append_extension(database, ".dmnd");
if (command == Config::view)
auto_append_extension(daa_file, ".daa");
if (compression == 1)
auto_append_extension(output_file, ".gz");
}
message_stream << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << " | by Benjamin Buchfink <*****@*****.**>" << endl;
message_stream << "Check http://github.com/bbuchfink/diamond for updates." << endl << endl;
#ifndef NDEBUG
verbose_stream << "Assertions enabled." << endl;
#endif
set_option(threads_, tthread::thread::hardware_concurrency());
switch (command) {
case Config::makedb:
case Config::blastp:
case Config::blastx:
case Config::view:
message_stream << "#CPU threads: " << threads_ << endl;
default:
;
}
if (command == Config::blastp || command == Config::blastx || command == Config::benchmark) {
if (tmpdir == "")
tmpdir = extract_dir(output_file);
if (gap_open == -1)
gap_open = 11;
if (gap_extend == -1)
gap_extend = 1;
score_matrix = Score_matrix(to_upper_case(matrix), gap_open, gap_extend, reward, penalty);
message_stream << "Scoring parameters: " << score_matrix << endl;
if (seg == "" && command == blastx)
seg = "yes";
verbose_stream << "SEG masking = " << (seg == "yes") << endl;
have_ssse3 = check_SSSE3();
if (have_ssse3)
verbose_stream << "SSSE3 enabled." << endl;
verbose_stream << "Reduction: " << Reduction::reduction << endl;
if (mode_more_sensitive) {
set_option(index_mode, 1u);
set_option(freq_sd, 200.0);
}
else if (mode_sensitive) {
set_option(index_mode, 1u);
set_option(freq_sd, 10.0);
}
else {
set_option(index_mode, 0u);
set_option(freq_sd, 50.0);
}
verbose_stream << "Seed frequency SD: " << freq_sd << endl;
::shapes = shape_config(index_mode, shapes);
verbose_stream << "Shape configuration: " << ::shapes << endl;
message_stream << "#Target sequences to report alignments for: ";
if (max_alignments == 0) {
max_alignments = std::numeric_limits<uint64_t>::max();
message_stream << "unlimited" << endl;
} else
message_stream << max_alignments << endl;
}
if (command == blastx)
input_value_traits = nucleotide_traits;
if (command == help)
parser.print_help();
/*log_stream << "sizeof(hit)=" << sizeof(hit) << " sizeof(packed_uint40_t)=" << sizeof(packed_uint40_t)
<< " sizeof(sorted_list::entry)=" << sizeof(sorted_list::entry) << endl;*/
}
/*!
*/
bool
Options::parseCmdLine( int argc,
char ** argv )
{
rcsc::ParamMap system_options( "System Options" );
rcsc::ParamMap window_options( "Window Options" );
rcsc::ParamMap editor_options( "Editor Options" );
rcsc::ParamMap view_options( "View Options" );
bool help = false;
bool version = false;
system_options.add()
( "help", "h",
rcsc::BoolSwitch( &help ),
"print this message." )
( "version", "v",
rcsc::BoolSwitch( &version ),
"print version." )
;
std::string geometry;
window_options.add()
( "maximize", "",
rcsc::BoolSwitch( &M_maximize ),
"start with a maximized window." )
( "full-screen", "",
rcsc::BoolSwitch( &M_full_screen ),
"start with a full screen window." )
( "geometry", "",
&geometry,
"specifies the window geometry \"[WxH][+X+Y]\". e.g. --geometry=1024x768+0+0" )
;
std::string conf_file;
std::string data_file;
std::string background_conf_file;
editor_options.add()
( "conf", "c",
&conf_file,
"specifies a .conf file." )
( "data", "d",
&data_file,
"specifies a .dat file." )
( "background-conf", "C",
&background_conf_file,
"specifies a .conf file as a background data." )
( "auto-backup", "",
&M_auto_backup,
"make backup files automatically" )
;
view_options.add()
( "no-antialiasing", "",
rcsc::NegateSwitch( &M_antialiasing ),
"disable antialiasing painting." )
( "no-auto-fit", "",
rcsc::NegateSwitch( &M_auto_fit_mode ),
"disable automatic view area fitting." )
;
rcsc::CmdLineParser parser( argc, argv );
parser.parse( system_options );
parser.parse( window_options );
parser.parse( editor_options );
parser.parse( view_options );
//
// analyze positional options
//
for ( std::vector< std::string >::const_iterator it = parser.positionalOptions().begin();
it != parser.positionalOptions().end();
++it )
{
// ".conf"
if ( it->length() > 5
&& it->compare( it->length() - 5, 5, ".conf" ) == 0 )
{
if ( conf_file.empty() )
{
conf_file = *it;
}
else if ( background_conf_file.empty() )
{
background_conf_file = *it;
}
else // if ( ! conf_file.empty() && ! background_conf_file.empty() )
{
help = true;
break;
}
}
else
{
help = true;
break;
}
}
M_conf_file = QString::fromStdString( conf_file );
M_data_file = QString::fromStdString( data_file );
M_background_conf_file = QString::fromStdString( background_conf_file );
//
// help message
//
if ( help
|| parser.failed()
|| parser.positionalOptions().size() > 4 )
{
std::cout << "Usage: " << "fedit"
<< " [options ... ] [conf file [background conf file]] [dat file]"
<< std::endl;
system_options.printHelp( std::cout, false ); // with_default = false
window_options.printHelp( std::cout );
editor_options.printHelp( std::cout );
view_options.printHelp( std::cout );
return false;
}
//
// version message
//
if ( version )
{
std::cout << "fedit" << " Version " << VERSION
<< std::endl;
return false;
}
//
// window size and position
//
parseWindowGeometry( geometry );
return true;
}
