args_t::args_t( int argc, const char * argv[] ) :
output( stdout ),
input1( stdin ),
input2( NULL ),
distance( DEFAULT_DISTANCE ),
min_distance( DEFAULT_MIN_DISTANCE ),
ambig( DEFAULT_AMBIG ),
format ( DEFAULT_FORMAT ),
overlap ( DEFAULT_OVERLAP ),
do_bootstrap( false ),
do_bootstrap_two_files ( false ),
do_count( false ),
quiet( false ),
do_fst( false ),
report_self ( false ),
counts_in_name ( DEFAULT_COUNTS_IN_NAME ),
include_prob( DEFAULT_INCLUDE_PROB ),
ambigs_to_resolve(NULL),
resolve_fraction(DEFAULT_FRACTION)
{
// skip arg[0], it's just the program name
for (int i = 1; i < argc; ++i ) {
const char * arg = argv[i];
if ( arg[0] == '-' && arg[1] == '-' ) {
if ( !strcmp( &arg[2], "help" ) ) help();
else if ( !strcmp( &arg[2], "version" ) ) version();
else
ERROR( "unknown argument: %s", arg );
}
else if ( arg[0] == '-' ) {
if ( !strcmp( &arg[1], "h" ) ) help();
else if ( arg[1] == 'v' ) version();
else if ( arg[1] == 'o' ) parse_output( next_arg (i, argc, argv) );
else if ( arg[1] == 't' ) parse_distance ( next_arg (i, argc, argv) );
else if ( arg[1] == 'w' ) parse_min_distance ( next_arg (i, argc, argv) );
else if ( arg[1] == 'l') parse_overlap( next_arg (i, argc, argv) );
else if ( arg[1] == 'f') parse_format( next_arg (i, argc, argv) );
else if ( arg[1] == 'a') parse_ambig( next_arg (i, argc, argv) );
else if ( arg[1] == 's') parse_second_in( next_arg (i, argc, argv) );
else if ( arg[1] == 'd') parse_counts_in_name( next_arg (i, argc, argv) );
else if ( arg[1] == 'u') parse_include_prob( next_arg (i, argc, argv) );
else if ( arg[1] == 'b') parse_bootstrap();
else if ( arg[1] == 'r') parse_bootstrap_two_files ();
else if ( arg[1] == 'c') parse_count();
else if ( arg[1] == 'q') parse_quiet();
else if ( arg[1] == 'm') parse_fst();
else if ( arg[1] == '0') parse_report_self();
else if ( arg[1] == 'g') parse_fraction( next_arg (i, argc, argv) );
else
ERROR( "unknown argument: %s", arg );
}
else
if (i == argc-1) {
parse_input (arg);
} else {
ERROR( "unknown argument: %s", arg );
}
}
}
args_t::args_t( int argc, const char * argv[] ) :
output( stdout ),
input( stdin ),
ambig( DEFAULT_AMBIG ),
data ( DEFAULT_DATA ),
counts_in_name ( DEFAULT_COUNTS_IN_NAME ),
quiet (false)
{
// skip arg[0], it's just the program name
for (int i = 1; i < argc; ++i ) {
const char * arg = argv[i];
if ( arg[0] == '-' && arg[1] == '-' ) {
if ( !strcmp( &arg[2], "help" ) ) help();
else
ERROR( "unknown argument: %s", arg );
}
else if ( arg[0] == '-' ) {
if ( !strcmp( &arg[1], "h" ) ) help();
else if ( arg[1] == 'o' ) parse_output( next_arg (i, argc, argv) );
else if ( arg[1] == 'a') parse_ambig( next_arg (i, argc, argv) );
else if ( arg[1] == 't') parse_data ( next_arg (i, argc, argv) );
else if ( arg[1] == 'd') parse_counts_in_name( next_arg (i, argc, argv) );
else if ( arg[1] == 'q') parse_quiet ( );
else
ERROR( "unknown argument: %s", arg );
}
else
if (i == argc-1) {
parse_input (arg);
} else {
ERROR( "unknown argument: %s", arg );
}
}
}