Bio::DB::Bam::AlignWrapper

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 <[email protected]>. <[email protected]> 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.