#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Introduce indels into sequences in the stream.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


use warnings;
use strict;
use Maasha::Common;
use Maasha::Biopieces;
use Maasha::Seq;


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


my ( $options, $in, $out, $insertions, $deletions, $seq_len, $record );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'insertions',         short => 'i', type => 'uint',  mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
        { long => 'insertions_percent', short => 'P', type => 'float', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
        { long => 'deletions',          short => 'd', type => 'uint',  mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
        { long => 'deletions_percent',  short => 'D', type => 'float', mandatory => 'no', default => 0, 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 ( $record->{ "SEQ" } )
    {
        $seq_len     = length $record->{ "SEQ" };

        $insertions  = $options->{ "insertions" } || int( $seq_len * ( $options->{ "insertions_percent" } / 100 ) );
        $deletions   = $options->{ "deletions" }  || int( $seq_len * ( $options->{ "deletions_percent" } / 100 ) );

        Maasha::Common::error( qq(insertions > sequence length: $insertions > $seq_len)  ) if $insertions > $seq_len;
        Maasha::Common::error( qq(deletions > sequence length: $deletions > $seq_len)  )   if $deletions > $seq_len;

        $record->{ "SEQ" } = Maasha::Seq::seq_insert( $record->{ "SEQ" }, $insertions );
        $record->{ "SEQ" } = Maasha::Seq::seq_delete( $record->{ "SEQ" }, $deletions );

        $record->{ "SEQ_LEN" } = length $record->{ "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();
}


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__