+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $new_record, $i );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'window_size', short => 'w', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => 0 },
+ { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+ {
+ $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+
+ for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
+ {
+ $new_record->{ "REC_TYPE" } = "BED";
+ $new_record->{ "CHR" } = $record->{ "CHR" };
+ $new_record->{ "CHR_BEG" } = $record->{ "CHR_BEG" } + $i;
+ $new_record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
+ $new_record->{ "BED_LEN" } = $options->{ "window_size" };
+ $new_record->{ "Q_ID" } = $record->{ "Q_ID" } . "_$i";
+ $new_record->{ "SCORE" } = $record->{ "SCORE" };
+ $new_record->{ "STRAND" } = $record->{ "STRAND" };
+
+ Maasha::Biopieces::put_record( $new_record, $out );
+ }
+ }
+ else
+ {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+