Bio::DB::Sam::Constants

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 <[email protected]>. <[email protected]> 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.