$options = Maasha::Biopieces::parse_options(
[
- { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'program', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => $progs_ok, disallowed => undef },
- { long => 'e_val', short => 'e', type => 'float', mandatory => 'no', default => 10, allowed => undef, disallowed => undef },
- { long => 'filter', short => 'f', type => 'string', mandatory => 'no', default => 'no', allowed => 'yes,no', disallowed => undef },
- { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
- { long => 'no_gaps', short => 'G', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'megablast', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'program', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => $progs_ok, disallowed => undef },
+ { long => 'e_val', short => 'e', type => 'float', mandatory => 'no', default => 10, allowed => undef, disallowed => undef },
+ { long => 'filter', short => 'f', type => 'string', mandatory => 'no', default => 'no', allowed => 'yes,no', disallowed => undef },
+ { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
+ { long => 'no_gaps', short => 'G', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'megablast', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'extend_threshold', short => 'E', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'word_size', short => 'W', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'single_hit', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
$options->{ 'megablast' } = 'F';
}
+if ( $options->{ 'single_hit' } ) {
+ $options->{ 'single_hit' } = 1
+} else {
+ $options->{ 'single_hit' } = 0
+}
+
if ( $options->{ 'verbose' } )
{
Maasha::Common::run(
"-i $tmp_in",
"-d $options->{ 'database' }",
"-F $options->{ 'filter' }",
+ "-P $options->{ 'single_hit' }",
+ "-W $options->{ 'word_size' }",
+ "-f $options->{ 'extend_threshold' }",
"-o $tmp_out",
),
1
"-i $tmp_in",
"-d $options->{ 'database' }",
"-F $options->{ 'filter' }",
+ "-P $options->{ 'single_hit' }",
+ "-W $options->{ 'word_size' }",
+ "-f $options->{ 'extend_threshold' }",
"-o $tmp_out",
"> /dev/null 2>&1"
),