- a -

• ADENINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t
• ADJACENCY_BIT : AMOS::Overlap_t, AMOS::Link_t
• ADJACENCY_BITS : AMOS::Overlap_t, AMOS::Link_t
• ALIGNMENT : AMOS::Link_t
• ANTINORMAL : AMOS::Overlap_t, AMOS::Link_t
• ANTINORMAL_BITS : AMOS::Overlap_t, AMOS::Link_t

- b -

• BAC : AMOS::Read_t, AMOS::Fragment_t
• BANK_VERSION : AMOS::Bank_t
• banktype_m : AMOS::Bank_t
• begin : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Message_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Range_t
• bid : AMOS::IDMap_t::HashTriple_t
• buffer_size_m : AMOS::Bank_t

- c -

• c : AMOS::IDMap_t::HashTriple_t
• COMPRESS_BIT : AMOS::Sequence_t
• CONTIG : AMOS::Read_t
• COVERAGE : AMOS::Feature_t
• curr_bid_m : AMOS::BankStream_t
• CYTOSINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t

- d -

• DEFAULT_BUFFER_SIZE : AMOS::BankStream_t, AMOS::Bank_t
• DEFAULT_PARTITION_SIZE : AMOS::Bank_t

- e -

• eid : AMOS::IDMap_t::HashTriple_t
• eid_m : AMOS::IBankable_t
• end : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Message_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Range_t
• END : AMOS::Read_t, AMOS::BankStream_t
• eof_m : AMOS::BankStream_t

- f -

• fix : AMOS::Bank_t::BankPartition_t
• fix_name : AMOS::Bank_t::BankPartition_t
• fix_size_m : AMOS::Bank_t
• FIX_STORE_SUFFIX : AMOS::Bank_t
• FLAGC_BIT : AMOS::Overlap_t
• flags_m : AMOS::IBankable_t

- g -

• gaps : AMOS::Tile_t
• GUANINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t

- i -

• idmap_m : AMOS::Bank_t
• IFO_STORE_SUFFIX : AMOS::Bank_t
• iid : AMOS::IDMap_t::HashTriple_t
• iid_m : AMOS::IBankable_t
• INNIE : AMOS::Overlap_t, AMOS::Link_t
• INNIE_BITS : AMOS::Overlap_t, AMOS::Link_t
• INSERT : AMOS::Fragment_t
• is_flagA : AMOS::BankFlags_t
• is_flagB : AMOS::BankFlags_t
• is_modified : AMOS::BankFlags_t
• is_open_m : AMOS::Bank_t
• is_removed : AMOS::BankFlags_t

- j -

• JOIN : AMOS::Feature_t

- l -

• last_bid_m : AMOS::Bank_t
• LCK_STORE_SUFFIX : AMOS::Bank_t
• length_m : AMOS::Sequence_t

- m -

• MAP_STORE_SUFFIX : AMOS::Bank_t
• MATEPAIR : AMOS::Link_t
• max_bid_m : AMOS::Bank_t
• MAX_LENGTH : AMOS::Kmer_t
• MAX_OPEN_PARTITIONS : AMOS::BankStream_t, AMOS::Bank_t
• max_partitions_m : AMOS::Bank_t
• mean : AMOS::Distribution_t
• mode_m : AMOS::Bank_t

- n -

• nbids_m : AMOS::Bank_t
• NCODE : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t
• nibble : AMOS::BankFlags_t
• NORMAL : AMOS::Overlap_t, AMOS::Link_t
• NORMAL_BITS : AMOS::Overlap_t, AMOS::Link_t
• npartitions_m : AMOS::Bank_t
• NULL_ADJACENCY : AMOS::Overlap_t, AMOS::Link_t
• NULL_FEATURE : AMOS::Feature_t
• NULL_FRAGMENT : AMOS::Fragment_t
• NULL_LINK : AMOS::Link_t
• NULL_READ : AMOS::Read_t

- o -

• offset : AMOS::Tile_t
• opened_m : AMOS::Bank_t
• ORF : AMOS::Feature_t
• OTHER : AMOS::Read_t, AMOS::Link_t, AMOS::Fragment_t
• OUTIE : AMOS::Overlap_t, AMOS::Link_t
• OUTIE_BITS : AMOS::Overlap_t, AMOS::Link_t
• OVERLAP : AMOS::Link_t

- p -

• partition_size_m : AMOS::Bank_t
• partitions_m : AMOS::Bank_t
• PHYSICAL : AMOS::Link_t
• POLYMORPHISM : AMOS::Feature_t

- q -

• QUAL_BITS : AMOS::Sequence_t
• qual_m : AMOS::Sequence_t

- r -

• range : AMOS::Tile_t
• READ_LOCK_CHAR : AMOS::Bank_t
• REPEAT : AMOS::Feature_t

- s -

• sd : AMOS::Distribution_t
• SEQ_BITS : AMOS::Sequence_t, AMOS::Kmer_t
• seq_m : AMOS::Sequence_t
• source : AMOS::Tile_t
• status_m : AMOS::Bank_t
• store_dir_m : AMOS::Bank_t
• store_pfx_m : AMOS::Bank_t
• SYNTENY : AMOS::Link_t

- t -

• THYMINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t
• tiles_m : AMOS::Layout_t
• TMP_STORE_SUFFIX : AMOS::Bank_t
• TRANSPOSON : AMOS::Read_t, AMOS::Fragment_t
• triples_m : AMOS::BankStream_t

- u -

• UNITIG : AMOS::Feature_t

- v -

• var : AMOS::Bank_t::BankPartition_t
• var_name : AMOS::Bank_t::BankPartition_t
• VAR_STORE_SUFFIX : AMOS::Bank_t

- w -

• WALK : AMOS::Read_t, AMOS::Fragment_t
• WRITE_LOCK_CHAR : AMOS::Bank_t

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