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.IX Title "Bio::DB::Bam::AlignWrapper 3pm"
.TH Bio::DB::Bam::AlignWrapper 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
Bio::DB::Bam::AlignWrapper \-\- Add high\-level methods to Bio::DB::Bam::Alignment
.SH SYNOPSIS
.IX Header "SYNOPSIS"
See Bio::DB::Bam::Alignment.
.SH DESCRIPTION
.IX Header "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.
.PP
.Vb 10
\& 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
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Constants
.SH AUTHOR
.IX Header "AUTHOR"
Lincoln Stein <lincoln.stein@oicr.on.ca>.
<lincoln.stein@bmail.com>
.PP
Copyright (c) 2009\-2015 Ontario Institute for Cancer Research.
.PP
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.