Bio::DB::HTS::Constants(3pm)

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