Command Line Arguments using qgenlib

Introduction

qgenlib provides a macro-based command line parsing library. This library was first implemented by Gonçalo Abecasis and used in many tools developed by Center for Statistical Genetics at the University of Michigan.

The key features of the command line parsing library is that the user can define the command line options using a simple macro and the library will automatically generate the help message and parse the command line arguments.

Example Usage

The following is a simple example to demonstrate how to use the command line parsing library.

#include <vector>
#include "qgenlib/params.h"
int main(int argc, char** argv) {
    // define the variables to store the command line arguments
    std::string str1;
    std::vector<std::string> str2;
    int int3 = 0;
    double double4 = 0.0;
    bool bool5 = false;

    // the macro definition starts with defining a paramList object.
    paramList pl;
    BEGIN_LONG_PARAMS(longParameters)
        LONG_PARAM_GROUP("Options for string arguments", NULL)
        LONG_STRING_PARAM("str1", &str1, "A dummy string argument")
        LONG_MULTI_STRING_PARAM("str2", &str2, "Another dummy string argument (can be specified multiple times)")

        LONG_PARAM_GROUP("Options for non-string arguments", NULL)
        LONG_INT_PARAM("int3", &int3, "A dummy integer argument")    
        LONG_DOUBLE_PARAM("double4", &double4, "A dummy double argument")
        LONG_PARAM("bool5",&bool5,"A dummy boolean argument")
    END_LONG_PARAMS();

    // 
    pl.Add(new longParams("Available Options", longParameters));
    pl.Read(argc, argv);
    pl.Status();

    printf("str1: %s\n", str1.c_str());
    printf("str2: ");
    for (int i = 0; i < str2.size(); i++) {
        printf("%s ", str2[i].c_str());
    }
    printf("\n");
    printf("int3: %d\n", int3);
    printf("double4: %f\n", double4);
    printf("bool5: %s\n", bool5 ? "true" : "false");

    return 0;
}

This example can also be found in the qbcf repository in the qbcf test-qgenlib tool.

Expected Output

Output of an example run with some parameter settings are shown as follows:

qbcf test-qgenlib --str1 10 --str2 abc --str2 def --int3 12345 --bool5
[qbcf test-qgenlib] -- Test basic functionalities in qgenlib

 Copyright (c) 2009-2022 by Hyun Min Kang and Adrian Tan
 Licensed under the Apache License v2.0 http://www.apache.org/licenses/

Available Options

The following parameters are available. Ones with "[]" are in effect:
       Options for string arguments : --str1 [10], --str2 [abc, def]
   Options for non-string arguments : --int3 [12345], --double4 [0.00],
                                      --bool5 [ON]

Run with --help for more detailed help messages of each argument.

str1: 10
str2: abc def 
int3: 12345
double4: 0.000000
bool5: true

Printing out the help message can be done with --help option as follows:

qbcf test-qgenlib --help                                              
[qbcf test-qgenlib] -- Test basic functionalities in qgenlib

 Copyright (c) 2009-2022 by Hyun Min Kang and Adrian Tan
 Licensed under the Apache License v2.0 http://www.apache.org/licenses/

Detailed instructions of parameters are available. Ones with "[]" are in effect:

Available Options:

== Options for string arguments ==
   --str1    [STR: ]             : A dummy string argument
   --str2    [V_STR: ]           : Another dummy string argument (can be specified multiple times)

== Options for non-string arguments ==
   --int3    [INT: 0]            : A dummy integer argument
   --double4 [FLT: 0.00]         : A dummy double argument
   --bool5   [FLG: OFF]          : A dummy boolean argument


NOTES:
When --help was included in the argument. The program prints the help message but do not actually run