Bio::DB::Bam::AlignWrapper -- Add high-level methods to 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
Lincoln Stein <email@example.com>. <firstname.lastname@example.org>
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.