NAME

FaSlice - FaSlice.pm from VCFTools

VERSION

version 1.123050

SYNOPSIS

use FaSlice;

my $fa = FaSlice->new(file=>'ref.fa'); $fa->get_base(1,12345); $fa->get_slice(1,12345,54321);

new

    About   : Creates new FaSlice object.
    Usage   : my $fa = FaSlice->new(file=>'ref.fa');
    Args    : file   .. the fasta file
              oob    .. out-of-bounds requests: one of 'throw' (throws), 'N' (fills the missing bases by Ns), or '' (returns empty string, default)
              size   .. size of the cached chunk read by samtools faidx (1_000_000)

get_base

    About   : Retrieves base at the given chromosome and position
    Usage   : my $fa = FaSlice->new(file=>'ref.fa'); $fa->get_base(1,12345);
    Args    : chromosome
              1-based coordinate

get_slice

    About   : Retrieves region
    Usage   : my $fa = FaSlice->new(file=>'ref.fa'); $fa->get_base(1,12345,54321);
    Args    : chromosome
              1-based coordinate

NAME

FaSlice.pm. Module for cached access to fasta sequences, employs samtools faidx.

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007