-my ( $options, $in, $out, $record, $data_in, $num, $entry );
-
-$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 => 'quality', short => 'q', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => undef },
- ]
-);
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-if ( $options->{ 'data_in' } )
-{
- $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
-
- $num = 1;
-
- while ( $entry = Maasha::Fastq::get_entry( $data_in ) )
- {
- if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
- {
- Maasha::Fastq::lowercase_low_scores( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'quality' } );
-
- $record->{ 'SCORES' } =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
- $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- last if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
-}
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );