Repository navigation
Expand file tree
/
Copy pathlambda.cpp
More file actions
118 lines (102 loc) · 3.85 KB
/
Copy pathlambda.cpp
File metadata and controls
118 lines (102 loc) · 3.85 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
// This file is part of Lambda.
//
// Lambda is Free Software: you can redistribute it and/or modify it
// under the terms found in the LICENSE[.md|.rst] file distributed
// together with this file.
//
// Lambda 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.
//
// ==========================================================================
// lambda.cpp: Main File for Lambda
// ==========================================================================
#include <sharg/all.hpp>
#include "mkindex.hpp"
#include "search.hpp"
#include "shared_options.hpp"
void parseCommandLineMain(int argc, char const ** argv);
int main(int argc, char const ** argv)
{
if (std::string(CMAKE_BUILD_TYPE) != "Release")
std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
int until = argc;
bool skipNext = false;
for (int i = 1; i < argc; ++i)
{
// version check expects a parameter
if (std::string(argv[i]) == "--version-check")
skipNext = true;
if (argv[i][0] != '-')
{
if (skipNext)
{
skipNext = false;
}
else
{
until = i + 1;
break;
}
}
}
try
{
parseCommandLineMain(until, argv);
}
catch (std::exception const & ext)
{
std::cerr << ext.what() << "\n";
return -1;
}
--until; // undo the "+ 1" above
std::string const subcommand_actual = argv[until];
if (subcommand_actual.starts_with("search"))
{
return searchMain(argc - until, argv + until);
}
else if (subcommand_actual.starts_with("mkindex"))
{
return mkindexMain(argc - until, argv + until);
}
else
{
// shouldn't be reached
std::cerr << "WRONG ARGUMENTS!\n";
return -1;
}
return 0;
}
void parseCommandLineMain(int argc, char const ** argv)
{
sharg::parser parser("lambda3", argc, argv, sharg::update_notifications::off);
parser.info.short_description = "Lambda, the Local Aligner for Massive Biological DatA.";
parser.info.synopsis.push_back("lambda3 [\\fIOPTIONS\\fP] COMMAND [\\fICOMMAND-OPTIONS\\fP]");
sharedSetup(parser);
std::string command{};
parser.add_positional_option(
command,
sharg::config{
.description = "The sub-program to execute. See above.",
.validator =
sharg::value_list_validator{"searchp", "searchn", "searchbs", "mkindexp", "mkindexn", "mkindexbs"}
});
parser.info.description.push_back("Available commands");
parser.info.description.push_back(
"\\fBsearchp \\fP– Perform a protein search (BLASTP, BLASTX, TBLASTN, TBLASTX).");
parser.info.description.push_back("\\fBsearchn \\fP– Perform a nucleotide search (BLASTN, MEGABLAST).");
parser.info.description.push_back("\\fBsearchbs \\fP– Perform a bisulfite search.");
parser.info.description.push_back("\\fBmkindexp \\fP– Create an index for protein searches.");
parser.info.description.push_back("\\fBmkindexn \\fP– Create an index for nucleotide searches.");
parser.info.description.push_back("\\fBmkindexbs\\fP– Create an index for bisulfite searches.");
parser.info.description.push_back(
"To view the help page for a specific command, simply run 'lambda command --help'.");
parser.parse();
}