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Lincoln D. Stein

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.