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# POD documentation - main docs before the code

=head1 NAME

GenOOx::Data::File::SAMbwa - GenOO framework extension to read SAM files created by the BWA aligner

=head1 SYNOPSIS

GenOO framework extension to read SAM files created by the BWA aligner.
Include it in your script and ask GenOO SAM parser to use it.

    use GenOOx::Data::File::SAMbwa::Record;

    my $file_parser = GenOO::Data::File::SAM->new(
        file          => 'file.sam',
        records_class => 'GenOOx::Data::File::SAMbwa::Record'
    );

    while (my $record = $file_parser->next_record) {
        # $record is now an instance of GenOOx::Data::File::SAMbwa::Record.
        print $record->cigar."\n"; # name
        print $record->flag."\n"; # flag
        print $record->number_of_mappings."\n"; # new stuff not present by default
    }


=head1 DESCRIPTION

The GenOO framework SAM parser avoids code that is unique to specific programs and makes no assumptions for the optional fields in a SAM file. This module is a plugin for the GenOO framework and provides the functionality for reading SAM files genera...

=head1 EXAMPLES

    # Create a parser
    my $file_parser = GenOO::Data::File::SAM->new(
        file          => 'file.sam',
        records_class => 'GenOOx::Data::File::SAMbwa::Record'
    );

    # Loop on the records of the file
    while (my $record = $file_parser->next_record) {
        # $record is now an instance of GenOOx::Data::File::SAMbwa::Record.
        print $record->cigar."\n"; # name
        print $record->flag."\n"; # flag
        print $record->number_of_mappings."\n"; # new stuff not present by default in GenOO
    }

=cut

# Let the code begin...

package GenOOx::Data::File::SAMbwa;
$GenOOx::Data::File::SAMbwa::VERSION = '0.0.5';

#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Modern::Perl;


1;