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lib/Alien/SeqAlignment/minimap2.pm  view on Meta::CPAN

use strict;
use warnings;

package Alien::SeqAlignment::minimap2;
$Alien::SeqAlignment::minimap2::VERSION = '0.02';
use parent qw( Alien::Base );
use Carp;
our $AUTOLOAD;

sub AUTOLOAD {
    my ($self) = @_;
    our $AUTOLOAD;
    $AUTOLOAD =~ s/.*::(\w+)$//;
    my $method = $1;
    unless ( exists $self->runtime_prop->{command}->{$method} ) {
        croak "Method $method not found";
    }
    else {
        no strict 'refs';
        *$AUTOLOAD = sub {
            shift->runtime_prop->{command}->{$method};
        };
    }
    use strict 'refs';
    goto &$AUTOLOAD;
}

=head1 NAME

Alien::SeqAlignment::minimap2 - A Perl wrapper for the minimap2 binary executables

=head1 VERSION

version 0.02

=head1 SYNOPSIS

To execute minimap2, you can use the following code:
  use Alien::SeqAlignment::minimap2;
  use Env qw( @PATH );
  unshift @PATH, Alien::SeqAlignment::hmmer3->bin_dir;

Then you can call the program as:

  Alien::SeqAlignment::minimap2->minimap2      (list of arguments)

=head1 DESCRIPTION

This distribution provides minimap2 so that it can be used by other
Perl distributions that are on CPAN.  The source code will be downloaded
from the github repository and installed in a private location if it is 
not already installed in your system.


=head1 METHODS

=head2 minimap2

 Alien::SeqAlignment::minimap2->minimap2            (list of arguments)

  
Returns the command name for running the CLI version of the minimap2 aligner.
Minimap2 uses a single executable to build the reference index and align the
query sequences.