Bio::DB::Sam::Constants.3pm

Langue: en

Version: 2010-05-25 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::DB::Sam::Constants -- Constants for use with SAM/BAM

SYNOPSIS

  use Bio::DB::Sam::Constants;
  my $pad_flag = BAM_CPAD;

DESCRIPTION

This module exports several constants for use with the SAM/BAM module. See the SAM documentation for their interpretation.
Cigar operations
   BAM_CIGAR_SHIFT
   BAM_CIGAR_MASK
   BAM_CMATCH
   BAM_CINS
   BAM_CDEL
   BAM_CREF_SKIP
   BAM_CSOFT_CLIP
   BAM_CHARD_CLIP
   BAM_CPAD
FLAGS
A hashref that maps flag values to human-readable names. For example: 
  FLAGS->{0x0008} == 'M_UNMAPPED'
RFLAGS
The reverse of FLAGS: 
  FLAGS->{M_UNMAPPED} == 0x0008

SEE ALSO

Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Alignment

AUTHOR

Lincoln Stein <lincoln.stein@oicr.on.ca>. <lincoln.stein@bmail.com>

Copyright (c) 2009 Ontario Institute for Cancer Research.

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.