Bio::DB::HTS::AlignWrapper3pm

Usage

Overview

This is a wrapper around Bio::DB::HTS::Alignment that adds the following high-level methods. These are described in detail in "High-level Bio::DB::HTS::Alignment methods" in Bio::DB::HTS::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