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Lincoln D. Stein


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


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


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


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


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.