Bio::DB::Sam::Constants(3pm)

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.