Bio::DB::HTS::Constants

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 <[email protected]<gt>

SEE ALSO

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