--- /dev/null
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+# Analyze mismatches and indels from ALIGN descriptors in the stream.
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Data::Dumper;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, @aligns, $align, $offset, $src, $dst, $data, $s_id, $pos, $count, $new_record );
+
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'min', short => 'm', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => '0' },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$data = {};
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( exists $record->{ 'ALIGN' } )
+ {
+ @aligns = split /,/, $record->{ 'ALIGN' };
+
+ foreach $align ( @aligns )
+ {
+ if ( $align =~ /(\d+):([ATCGN-])>([ATCGN-])/ )
+ {
+ $offset = $1;
+ $src = $2;
+ $dst = $3;
+
+ $data->{ $record->{ 'S_ID' } }->{ $record->{ 'S_BEG' } + $offset }->{ $src }->{ $dst }++;
+ }
+ }
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+foreach $s_id ( sort keys %{ $data } )
+{
+ foreach $pos ( sort { $a <=> $b } keys %{ $data->{ $s_id } } )
+ {
+ foreach $src ( sort keys %{ $data->{ $s_id }->{ $pos } } )
+ {
+ foreach $dst ( sort keys %{ $data->{ $s_id }->{ $pos }->{ $src } } )
+ {
+ $count = $data->{ $s_id }->{ $pos }->{ $src }->{ $dst };
+
+ if ( $count >= $options->{ 'min' } )
+ {
+ $new_record->{ 'REC_TYPE' } = "SNP";
+ $new_record->{ 'S_ID' } = $s_id;
+ $new_record->{ 'S_POS' } = $pos;
+ $new_record->{ 'SRC' } = $src;
+ $new_record->{ 'DST' } = $dst;
+ $new_record->{ 'SNP_COUNT' } = $count;
+
+ if ( $src eq '-' ) {
+ $new_record->{ 'TYPE' } = "INSERTION";
+ } elsif ( $dst eq '-' ) {
+ $new_record->{ 'TYPE' } = "DELETION";
+ } else {
+ $new_record->{ 'TYPE' } = "MISMATCH";
+ }
+
+ Maasha::Biopieces::put_record( $new_record, $out );
+ }
+ }
+ }
+ }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__