Bio::DB::Sam::ConstantUser Contributed Perl DocumentBio::DB::Sam::Constants(3)NAMEBio::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.
perl v5.14.2 2012-08-23 Bio::DB::Sam::Constants(3)