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