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.