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
|
/*
* File: kmdsCmdLine.cpp
*
* Reads command line input to kmds
*
*/
#include "kmds.hpp"
namespace po = boost::program_options; // Save some typing
// Use boost::program_options to parse command line input
// This does pretty much all the parameter checking needed
int parseCommandLine (int argc, char *argv[], po::variables_map& vm)
{
int failed = 0;
//Required options
po::options_description required("Required options");
required.add_options()
("kmers,k", po::value<std::string>(), "dsm kmer output file (not needed if using --mds_concat)")
("pheno,p", po::value<std::string>(), ".pheno metadata");
po::options_description mds("MDS options");
mds.add_options()
("output,o", po::value<std::string>(), "output prefix for new dsm file")
("no_mds", "do not perform MDS; output subsampled matrix instead")
("write_distances", "write csv of distance matrix")
("mds_concat", po::value<std::string>(), "list of subsampled matrices to use in MDS. Performs only MDS; implies --no_filtering")
("pc", po::value<int>()->default_value(pc_default), "number of principal coordinates to output")
("size", po::value<long int>()->default_value(size_default), "number of kmers to use in MDS")
("threads", po::value<int>()->default_value(1), ("number of threads. Suggested: " + std::to_string(std::thread::hardware_concurrency())).c_str());
//Optional filtering parameters
//NB pval cutoffs are strings for display, and are converted to floats later
po::options_description filtering("Filtering options");
filtering.add_options()
("no_filtering", "turn off all filtering and do not output new kmer file")
("max_length", po::value<long int>()->default_value(max_length_default), "maximum kmer length")
("maf", po::value<double>()->default_value(maf_default), "minimum kmer frequency")
("min_words", po::value<int>(), "minimum kmer occurrences. Overrides --maf");
po::options_description other("Other options");
other.add_options()
("version", "prints version and exits")
("help,h", "full help message");
po::options_description all;
all.add(required).add(mds).add(filtering).add(other);
try
{
po::store(po::command_line_parser(argc, argv).options(all).run(), vm);
if (vm.count("help"))
{
printHelp(all);
failed = 1;
}
else if (vm.count("version"))
{
std::cout << VERSION << std::endl;
failed = 1;
}
else
{
po::notify(vm);
failed = 0;
// Check input files exist, and can stat
if ((vm.count("kmers") && !fileStat(vm["kmers"].as<std::string>())) || (vm.count("pheno") && !fileStat(vm["pheno"].as<std::string>())))
{
failed = 1;
}
}
}
catch (po::error& e)
{
// Report errors from boost library
std::cerr << "Error in command line input: " << e.what() << "\n";
std::cerr << "Run 'kmds --help' for full option listing\n\n";
std::cerr << required << "\n" << other << "\n";
failed = 1;
}
return failed;
}
// Print long help message
void printHelp(po::options_description& help)
{
std::cerr << "kmds" << "\n";
std::cerr << "\t1) filter and subsample with --no_mds and --size\n";
std::cerr << "\t2) combine, and do metric multidimensional scaling with --mds_concat\n";
std::cerr << help << "\n";
}
|
