+use Maasha::Biopieces;
+use Maasha::Align;
+
+use constant {
+ SEQ_NAME => 0,
+ SEQ => 1,
+};
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, @entries, $entry );
+
+$options = Maasha::Biopieces::parse_options();
+
+$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->{ "SEQ_NAME" } and $record->{ "SEQ" } ) { # TODO use biopieces2fasta() instead
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
+ } else {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+@entries = Maasha::Align::align( \@entries );
+
+foreach $entry ( @entries )
+{
+ if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
+ {
+ $record = {
+ SEQ_NAME => $entry->[ SEQ_NAME ],
+ SEQ => $entry->[ SEQ ],
+ SEQ_LEN => length $entry->[ SEQ ],
+ };
+
+ 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();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+