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#adjust_scoring_matrix PasvLib::Alignment
#alignment_columns PasvLib::Alignment
#date_and_time PasvLib::CoreExtensions::Time
#gap? PasvLib::Alignment
#geometric_index PasvLib::Alignment
#geometric_score PasvLib::Alignment
#get_oligo PasvLib::Utils
#get_type PasvLib::Utils
#pos_to_gapped_pos PasvLib::Utils
#read_queries PasvLib::Io
#read_refs PasvLib::Io
#run_and_time_it! PasvLib::CoreExtensions::Process
#run_it PasvLib::CoreExtensions::Process
#run_it! PasvLib::CoreExtensions::Process
#similarity_score PasvLib::Alignment
#spans_end PasvLib::Utils
#spans_start PasvLib::Utils
#time_it PasvLib::CoreExtensions::Time
#to_binary_matrix PasvLib::Alignment