#!/usr/bin/env perl
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Sort records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
use warnings;
use strict;
-
use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i, $ok );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'reverse', short => 'r', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+foreach $key ( @{ $options->{ "keys" } } )
+{
+ if ( $key =~ s/n$// ) {
+ push @sort_cmd, qq(\$a->{ "$key" } <=> \$b->{ "$key" });
+ } else {
+ push @sort_cmd, qq(\$a->{ "$key" } cmp \$b->{ "$key" });
+ }
+}
+
+$sort_str = join " or ", @sort_cmd;
+$sort_sub = eval "sub { $sort_str }"; # NB security issue!
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ $ok = 1;
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( not exists $record->{ $key } )
+ {
+ $ok = 0;
+ last;
+ }
+ }
+
+ push @records, $record if $ok;
+}
+
+@records = sort $sort_sub @records;
+
+if ( $options->{ "reverse" } )
+{
+ for ( $i = scalar @records - 1; $i >= 0; $i-- ) {
+ Maasha::Biopieces::put_record( $records[ $i ], $out );
+ }
+}
+else
+{
+ for ( $i = 0; $i < scalar @records; $i++ ) {
+ Maasha::Biopieces::put_record( $records[ $i ], $out );
+ }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__