Bio::DB::HTS::Constants

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

 use Bio::DB::HTS::Constants;
 my $pad_flag = BAM_CPAD;

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
    

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

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