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) 2009-2015 Ontario Institute for Cancer Research.

       This package and its accompanying libraries are free software; you can redistribute it
       and/or modify it under the terms of the Artistic License 2.0, the Apache 2.0 License, or
       the GNU General Public License (version 1 or higher).  Refer to LICENSE for the full
       license text.