Copyright [2015-2018] EMBL-European Bioinformatics Institute
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Bio::DB::HTS::AlignWrapper -- Add high-level methods to Bio::DB::HTS::Alignment
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
Rishi Nag <firstname.lastname@example.org<gt>