+use Maasha::Biopieces;
+use Maasha::Match;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, @entries, $results, $tmp_dir );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => 0 },
+ { long => 'direction', short => 'd', type => 'string', mandatory => 'no', default => 'both', allowed => 'both,forward,reverse', disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( @entries == 1 )
+{
+ $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $tmp_dir );
+
+ map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
+}
+else
+{
+ $results = Maasha::Match::match_mummer( [ shift @entries ], \@entries, $options, $tmp_dir );
+
+ map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+