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 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.