NAME

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

SYNOPSIS

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

use GenOOx::Data::File::SAMstar::Record;

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

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

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 generated from the STAR aligner. The module has been created on top of the generic GenOO SAM parser and to use it just include it in your scripts and ask GenOO SAM parser to use it.

EXAMPLES

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

# Loop on the records of the file
while (my $record = $file_parser->next_record) {
    # $record is now an instance of GenOOx::Data::File::SAMstar::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
}