LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

NAME

Bio::DB::HTS::Constants -- Constants for use with SAM/BAM

SYNOPSIS

use Bio::DB::HTS::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:

RFLAGS->{M_UNMAPPED} == 0x0008

AUTHOR

Rishi Nag <rishi@ebi.ac.uk<gt>

SEE ALSO

Bio::Perl, Bio::DB::HTS, Bio::DB::Bam::Alignment