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#<=> Bio::Mutation
call_mutations MutationsCLI
call_mutations_given_product MutationsCLI
#combine_adjacent Bio::Alignment::CIGAR
consequences_for_transcript VepHgvs
construct_products MutationsCLI
#count MutantAllele
#cumulative Bio::DB::Tag::MD
default_species MutationsCLI
#deleted_length Bio::Alignment::CIGAR
#deletions Bio::DB::Tag::MD
#example MutantAllele
#hgnc Bio::Alignment::CIGAR
#initialize Bio::Alignment::CIGAR
#initialize Bio::Mutation
#initialize MutantAllele
#initialize Bio::DB::Tag::MD
#inserted_length Bio::Alignment::CIGAR
#lookup MutantAllele
#masked_length Bio::Alignment::CIGAR
#matched_length Bio::Alignment::CIGAR
#mutant Bio::Mutation
#mutations MutantAllele
not_included_file? MutationsCLI
#pairs Bio::Alignment::CIGAR
#pairs Bio::DB::Tag::MD
#position Bio::Mutation
#positions Bio::Alignment::CIGAR
previous_lookups MutantAllele
#query Bio::Alignment::CIGAR
#query_length Bio::Alignment::CIGAR
query_operations Bio::Alignment::CIGAR
#reconstruct_tag Bio::DB::Tag::MD
#ref_length Bio::DB::Tag::MD
#reference Bio::Mutation
#reference Bio::Alignment::CIGAR
#reference_length Bio::Alignment::CIGAR
reference_operations Bio::Alignment::CIGAR
regexps Bio::Alignment::CIGAR
#remove_empty! Bio::Alignment::CIGAR
#remove_small! Bio::Alignment::CIGAR
#report Bio::DB::Tag::MD
#seq MutantAllele
#seqname Bio::Mutation
set_defaults MutationsCLI
#slice Bio::DB::Tag::MD
#subalignment Bio::Alignment::CIGAR
#subcigar Bio::Alignment::CIGAR
subexp Bio::Alignment::CIGAR
#substitutions Bio::DB::Tag::MD
#tag SamMutationCLI
tag MutationsCLI
#tag Bio::DB::Tag::MD
tag_to_add MutationsCLI
#to_hgvs Bio::MutationArray
#to_hgvs Bio::Mutation
#to_json Bio::Mutation
#to_yaml Bio::Mutation
#type Bio::Mutation
#unmasked Bio::Alignment::CIGAR
#vep VepHgvs