adding bzip2 support in ruby

[biopieces.git] / bp_bin / uniq_vals

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..c9af962ad6b5a58ec21e1cac6c2132eb31734316 100755 (executable)
--- a/bp_bin/uniq_vals
+++ b/bp_bin/uniq_vals
@@ -1,6 +1,96 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Select unique or non-unique records from the stream based on the value of a given key.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, %hash, $record );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'key',    short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'invert', short => 'i', 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" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( exists $record->{ $options->{ "key" } } )
+    {
+        if ( not $hash{ $record->{ $options->{ "key" } } } and not $options->{ "invert" } )
+        {
+            Maasha::Biopieces::put_record( $record, $out );
+
+            $hash{ $record->{ $options->{ "key" } } } = 1;
+        }
+        elsif ( $hash{ $record->{ $options->{ "key" } } } and $options->{ "invert" } )
+        {
+            Maasha::Biopieces::put_record( $record, $out );
+        }
+        else
+        {
+            $hash{ $record->{ $options->{ "key" } } } = 1;
+        }
+    }
+    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();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__