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.