Bio::DB::Bam::AlignWrapper.3pm

Langue: en

Version: 2010-05-25 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::DB::Bam::AlignWrapper -- Add high-level methods to Bio::DB::Bam::Alignment

SYNOPSIS

See Bio::DB::Bam::Alignment.

DESCRIPTION

This is a wrapper around Bio::DB::Bam::Alignment that adds the following high-level methods. These are described in detail in ``High-level Bio::DB::Bam::Alignment methods'' in Bio::DB::Bam::Alignment.
  add_segment()         add a new subfeature to split alignments
  get_SeqFeatures()     fetch subfeatures from split alignments
  split_splices()       process cigar strings to produce split alignments
  expand_flags()        return true if flags should be expanded into tags
  seq_id()              return human-readable reference sequence name
  seq()                 return Bio::PrimarySeq object for reference sequence
  subseq()              return a subsequence across the indicated range
  dna()                 return the DNA of the reference sequence
  attributes()          synonym for get_tag_values()
  get_all_tags()        return all tag names
  get_tag_values()      return the values of the given tag
  has_tag()             return true if the given tag is defined
 
 

SEE ALSO

Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Constants

AUTHOR

Lincoln Stein <lincoln.stein@oicr.on.ca>. <lincoln.stein@bmail.com>

Copyright (c) 2009 Ontario Institute for Cancer Research.

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.