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) 2009-2015 Ontario Institute for Cancer Research.

This package and its accompanying libraries are free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0, the Apache 2.0 License, or the GNU General Public License (version 1 or higher). Refer to LICENSE for the full license text.