void inventory_selector::add_custom_items( const std::list<item>::const_iterator &from,
const std::list<item>::const_iterator &to,
const std::string &title,
const std::function<std::shared_ptr<item_location>( item * )> &locator )
{
const auto &stacks = restack_items( from, to );
for( const auto &stack : stacks ) {
const auto &location = locator( stack.front() );
if( filter( *location ) ) {
const std::string name = trim( string_format( _( "%s %s" ), to_upper_case( title ).c_str(),
direction_suffix( u.pos(), location->position() ).c_str() ) );
if( categories.empty() || categories.back().id != name ) {
categories.emplace_back( name, name, INT_MIN + int( categories.size() ) );
}
if( custom_column == nullptr ) {
custom_column.reset( new inventory_column() );
}
const long invlet = ( cur_custom_invlet <= max_custom_invlet ) ? cur_custom_invlet++ : '\0';
custom_column->add_entry( inventory_entry( location, stack.size(), &categories.back(), c_unset, invlet ) );
}
}
}
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;*/
}
void shift_string(char *string) {
int i;
for(i = 0; i < strlen(string); i++)
string[i] = to_upper_case(string[i]);
}
inline static dt::istring call(vm_heap &heap, const dt::istring &input) { return to_upper_case(heap, input); }
