#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Assemble tag contigs from overlapping BED type records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::UCSC::BED;
+
+use constant {
+ chrom => 0, # BED field names
+ chromStart => 1,
+ chromEnd => 2,
+ name => 3,
+ score => 4,
+ strand => 5,
+ thickStart => 6,
+ thickEnd => 7,
+ itemRgb => 8,
+ blockCount => 9,
+ blockSizes => 10,
+ blockStarts => 11,
+};
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $tmp_dir, $fh_in, $fh_out, $cols, $record, $bed_entry, %fh_hash, %file_hash, $file, $strand, $id, $tag_file, $bed_file );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+`cd "$ENV{ BP_C }/Maasha/src" && make`; # FIXME OMG this is crufty!
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$cols = 6; # we only need the first 6 BED columns
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) )
+ {
+ if ( not exists $fh_hash{ $bed_entry->[ chrom ] . $bed_entry->[ strand ] } )
+ {
+ $file = "$tmp_dir/$bed_entry->[ chrom ]$bed_entry->[ strand ]";
+
+ $file_hash{ $bed_entry->[ chrom ] . $bed_entry->[ strand ] } = $file;
+ $fh_hash{ $bed_entry->[ chrom ] . $bed_entry->[ strand ] } = Maasha::Filesys::file_write_open( $file );
+ }
+
+ $fh_out = $fh_hash{ $bed_entry->[ chrom ] . $bed_entry->[ strand ] };
+
+ Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } );
+ }
+}
+
+$id = 0;
+
+foreach $file ( sort keys %file_hash )
+{
+ $bed_file = $file_hash{ $file };
+ $tag_file = "$bed_file.tc";
+
+ $strand = substr $file, -1, 1;
+
+ Maasha::Common::run( "bed2tag_contigs", "< $bed_file > $tag_file" );
+
+ $fh_in = Maasha::Filesys::file_read_open( $tag_file );
+
+ while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $fh_in, $cols, $options->{ 'check' } ) )
+ {
+ $bed_entry->[ name ] = sprintf( "TC%08d", $id );
+ $bed_entry->[ strand ] = $strand;
+
+ if ( $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry ) ) {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+
+ $id++;
+ }
+
+ close $fh_in;
+
+ unlink $bed_file;
+ unlink $tag_file;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__