Table of Contents - bio-sam-mutation-0.4.1 Documentation
Pages
Classes and Modules
- Bio
- Bio::Alignment
- Bio::Alignment::CIGAR
- Bio::Alignment::IteratePairs
- Bio::DB
- Bio::DB::Tag
- Bio::DB::Tag::MD
- Bio::Mutation
- Bio::MutationArray
- MutantAllele
- MutationsCLI
- Object
- VepHgvs
Methods
- ::call_mutations — MutationsCLI
- ::call_mutations_given_product — MutationsCLI
- ::consequences_for_transcript — VepHgvs
- ::construct_products — MutationsCLI
- ::new — Bio::Alignment::CIGAR
- ::new — Object
- ::new — Bio::DB::Tag::MD
- ::new — MutantAllele
- ::new — Bio::Mutation
- ::not_included_file? — MutationsCLI
- ::set_defaults — MutationsCLI
- ::tag — MutationsCLI
- #<=> — Bio::Mutation
- #add_tag — Object
- #add_tag! — Object
- #combine_adjacent — Bio::Alignment::CIGAR
- #count_type — Bio::Alignment::CIGAR
- #deleted_length — Bio::Alignment::CIGAR
- #deletions — Bio::DB::Tag::MD
- #deletions_to_matches — Bio::Alignment::CIGAR
- #hgnc — Bio::Alignment::CIGAR
- #inserted_length — Bio::Alignment::CIGAR
- #iterate_pairs — Bio::Alignment::IteratePairs
- #lookup — MutantAllele
- #masked_length — Bio::Alignment::CIGAR
- #matched_length — Bio::Alignment::CIGAR
- #mutations — Object
- #positions — Bio::Alignment::CIGAR
- #query — Bio::Alignment::CIGAR
- #query — Object
- #query_length — Bio::Alignment::CIGAR
- #reconstruct_tag — Bio::DB::Tag::MD
- #ref_length — Bio::DB::Tag::MD
- #reference_length — Bio::Alignment::CIGAR
- #regenerate_string — Object
- #remove_empty! — Bio::Alignment::CIGAR
- #remove_small! — Bio::Alignment::CIGAR
- #remove_small_nonmatches — Bio::Alignment::CIGAR
- #report — Bio::DB::Tag::MD
- #slice — Bio::Alignment::CIGAR
- #slice — Bio::DB::Tag::MD
- #subalignment — Bio::Alignment::CIGAR
- #subcigar — Bio::Alignment::CIGAR
- #substitutions — Bio::DB::Tag::MD
- #to_hgvs — Bio::Mutation
- #to_hgvs — Bio::MutationArray
- #to_json — Bio::Mutation
- #to_yaml — Bio::Mutation
- #unmasked — Bio::Alignment::CIGAR
- #vep — VepHgvs