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
        mate_seq_id()         return human-readable mate reference sequence name
        dna()                 return the DNA of the reference sequence
        tam_line()            return the text representation of the alignment
        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.