$options = Maasha::Biopieces::parse_options(
[
- { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
- { long => 'format', short => 'f', type => 'string', mandatory => 'no', default => 'octal', allowed => 'octal,decimal', disallowed => undef },
- { long => 'quality', short => 'q', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => undef },
- { long => 'skip_scores', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ { long => 'format', short => 'f', type => 'string', mandatory => 'no', default => 'octal', allowed => 'octal,decimal', disallowed => undef },
+ { long => 'quality', short => 'q', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => undef },
+ { long => 'skip_quality', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
{
if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
{
- if ( not $options->{ 'skip_scores' } )
+ if ( not $options->{ 'skip_quality' } )
{
$record->{ 'SCORES' } =~ s/(\d+) ?/Maasha::Fastq::score2phred( $1 )/ge if $options->{ 'format' } eq 'decimal';
Maasha::Fastq::solexa2phred( $record->{ 'SCORES' } );