Here is a list of all documented class members with links to the class documentation for each member:

- a -

• accessory() : shore::read::accessory , shore::alignment::accessory
• add_codec() : shore::istreams , shore::ostreams
• add_file() : shore::uncaught_handler
• add_fragment() : shore::frag_vector< Iterator >
• add_key() : shore::cmp_tokens
• add_option() : shore::program , shore::av_parser , shore::program
• add_paired() : shore::alignment_builder
• add_plugin() : shore::buffer_chain< T >
• add_qry() : shore::alignment_builder
• add_ref() : shore::dp_multialigner_pipe< RefIter, QryIter, Scoring > , shore::alignment_builder
• add_residualargs() : shore::av_parser , shore::program
• add_softclip() : shore::alignment_builder
• add_stream() : shore::uncaught_handler
• alias : shore::annotation_entry
• alignment() : shore::alignment
• alignment_builder_type : shore::dp_traits< RefType, QryType >
• alignment_id : shore::dp_trace
• alignment_matrix : shore::dp_alignment< RefIter, QryIter, Scoring >
• alignment_string : shore::dp_trace , shore::alignment
• alignment_trimmer_pipe() : shore::alignment_trimmer_pipe
• allow_mpi() : shore::program
• allows_options() : shore::av_parser
• allows_residualargs() : shore::av_parser
• amb() : shore::nuc
• append() : shore::intpack , shore::incremental_mean_var , shore::feed< T >
• apply() : shore::plugin< T > , shore::sorting_check< T, Cmp >
• arg_format() : shore::opt_base , shore::av_option< std::pair< T, U > > , shore::opt_base1< T >
• argdefault_string() : shore::av_option< unary > , shore::av_option< std::vector< T > > , shore::av_option< bool > , shore::opt_base2< T > , shore::opt_base , shore::av_option< std::vector< std::vector< T > > > , shore::av_option< std::pair< T, U > > , shore::av_option< std::set< T > >
• array_begin() : shore::suffix_index
• array_end() : shore::suffix_index
• ASCIIENC_CHASTITY : shore::read
• ASCIIENC_ILLUMINA : shore::read
• ASCIIENC_SANGER : shore::read
• aux_info : shore::opt_base