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# GenOOx-Data-File-SAMstar

## Summary
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.

## 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...

## Example
```perl
# 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
}
```

## Installation
* **Using CPAN** - Easier
  1. If you have cpanm installed. `cpanm GenOOx::Data::File::SAMstar`.
  2. If you do not have cpanm. See [here](http://www.cpan.org/modules/INSTALL.html).
* **Using Git** - Preferred so you may contribute
  1. Install git ([directions](http://git-scm.com/downloads)).
  2. Install dependencies (listed below) from CPAN. [How to install CPAN modules](http://www.cpan.org/modules/INSTALL.html).
  3. Clone the GenOO repository on your machine
     `git clone git@github.com:genoo/GenOOx-Sam-STAR.git`.
  4. To verify that everything works 
     `cd path/to/your/clone/; prove -l t/*.t;`.
  5. In the beginning of your perl script write the following
     `use lib 'path/to/your/clone/lib/'`.

## Dependencies (maybe not exhaustive)
* GenOO
* Modern::Perl
* Moose

## Copyright
Copyright (c) 2013 Emmanouil Maragkakis and Panagiotis Alexiou.

## License
This library is free software and may be distributed under the same terms as perl itself.

This library 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.