jellyfish

o*Deprecated List

o+Class List

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >

|o*jellyfish::aligned_values::array< _key_t, _val_t, atomic, mem_block_t >

|o*jellyfish::direct_indexing::array< key_t, val_t, atomic_t, mem_block_t >

|o*arys_iterator< Key, Val, A >

|o*arys_t< Key, Val, nb, shift, mask >

|o*bad_size_exception

|o*locks::pthread::barrier

|o*counter_t::block

|o*jellyfish::capped_integer< T >

|o*jellyfish::circular_buffer< T >

|o*cite_args

|o*cite_cmdline_params

|o*cmd_func

|o*err::code

|o*jellyfish::compacted_dumper< storage_t, atomic_t >

|o*concurrent_queue< Val >

|o*locks::pthread::cond

|o*counter_t

|o*err::die_t

|o*jellyfish::direct_sorted_dumper< storage_t, atomic_t >

|o*display_kmer

|o*divisor64

|o*jellyfish::double_fifo_input< T >

|o*dump_args

|o*dump_cmdline_params

|o*dump_fastq_main_args

|o*dump_fastq_main_cmdline_params

|o*jellyfish::raw_hash::dumper< storage_t >

|o*jellyfish::dumper_t

|o*arys_t< Key, Val, nb, shift, mask >::elt

|o*ErrorWriting

|o*jellyfish::fasta_read_parser

|o*jellyfish::fasta_sequence_parser

|o*jellyfish::fastq_read_parser

|o*jellyfish::fastq_seq_qual_parser

|o*jellyfish::fastq_sequence_parser

|o*jellyfish::file_parser

|o*jellyfish::Float

|o*jellyfish::Float::float_int

|o*atomic::gcc

|o*generate_sequence_args

|o*generate_sequence_cmdline_params

|o*generic_list

|o*generic_value

|o*half

|o*jellyfish::hash< key_t, val_t, ary_t, atomic >

|o*hash_fastq_merge_args

|o*hash_fastq_merge_cmdline_params

|o*hash_merge_args

|o*hash_merge_cmdline_params

|o*jellyfish::hash_t

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >::header

|o*jellyfish::fastq_hash::header

|o*jellyfish::compacted_hash::header

|o*jellyfish::raw_hash::header

|o*jellyfish::heap_item_compare< iterator >

|o*jellyfish::heap_item_t< iterator >

|o*jellyfish::heap_t< iterator >

|o*histo_args

|o*histo_cmdline_params

|o*histo_fastq_main_args

|o*histo_fastq_main_cmdline_params

|o*histogram< hash_t >

|o*jellyfish::compacted_hash::query< key_t, val_t >::iterator

|o*jellyfish::aligned_values::array< _key_t, _val_t, atomic, mem_block_t >::iterator

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >::iterator

|o*jellyfish::direct_indexing::array< key_t, val_t, atomic_t, mem_block_t >::iterator

|o*lazy_mapped_file_t

|o*lazy_mapped_files_t

|o*locking_hash_counter< Key, Val, arys_t >

|o*allocators::malloc

|o*mapped_file

|o*mapped_files_t

|o*mer_counter_args

|o*mer_counter_cmdline_params

|o*mer_counting< parser_t, hash_t >

|o*mer_counting_base

|o*mer_counting_fasta_direct

|o*mer_counting_fasta_hash

|o*mer_counting_quake

|o*mer_counting_qual_fasta_hash

|o*allocators::mmap

|o*locks::pthread::mutex

|o*dbg::no_flush

|o*dbg::no_print_t

|o*err::no_t

|o*jellyfish::noop_dumper

|o*jellyfish::Offsets< word >::offset_pair_t

|o*jellyfish::Offsets< word >::offset_t

|o*jellyfish::Offsets< word >

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >::overlap_iterator

|o*jellyfish::parse_dna

|o*jellyfish::parse_quake

|o*jellyfish::parse_qual_dna

|o*jellyfish::parse_read

|o*parser

|o*dbg::print_t

|o*jellyfish::compacted_hash::query< key_t, val_t >

|o*jellyfish::raw_hash::query< _storage_t >

|o*query_args

|o*query_cmdline_params

|o*err::raise_t< err_t >

|o*jellyfish::fastq_hash::raw_dumper< storage_t >

|o*rDNAg_t

|o*jellyfish::read_parser

|o*jellyfish::read_parser::read_t

|o*jellyfish::compacted_hash::reader< key_t, val_t >

|o*jellyfish::read_parser::reads_t

|o*jellyfish::invertible_hash::reprobe_limit_t

|o*locks::pthread::Semaphore

|o*jellyfish::seq_qual_parser

|o*jellyfish::sequence_parser

|o*jellyfish::seq_qual_parser::sequence_t

|o*jellyfish::sequence_parser::sequence_t

|o*allocators::shm

|o*jellyfish::simple_growing_array< T >

|o*jellyfish::sorted_dumper< storage_t, atomic_t >

|o*SquareBinaryMatrix

|o*stats

|o*stats_args

|o*stats_cmdline_params

|o*jellyfish::storage_t

|o*dbg::str

|o*dbg::stringbuf

|o*err::substr

|o*jellyfish::parse_read::thread

|o*jellyfish::parse_quake::thread

|o*jellyfish::parse_qual_dna::thread

|o*jellyfish::hash< key_t, val_t, ary_t, atomic >::thread

|o*jellyfish::parse_dna::thread

|o*thread_exec

|o*thread_hash_counter< Key, Val, arys_t >

|o*thread_exec::thread_info

|o*jellyfish::compacted_dumper< storage_t, atomic_t >::thread_info_t

|o*jellyfish::raw_hash::dumper< storage_t >::thread_info_t

|o*jellyfish::sorted_dumper< storage_t, atomic_t >::thread_info_t

|o*jellyfish::direct_sorted_dumper< storage_t, atomic_t >::thread_info_t

|o*jellyfish::hash< key_t, val_t, ary_t, atomic >::thread_ptr_t

|o*Time

|o*allocators::mmap::tinfo

|o*token_ring< cond_t >::token

|o*token_ring< cond_t >

|o*Tptr< T >

|o*half::uif

|o*jellyfish::compacted_hash::writer< storage_t >

|o*writer_buffer

|o*writer_info

|\*dbg::xspace

o+Class Hierarchy

|o*jellyfish::direct_indexing::array< key_t, val_t, atomic_t, mem_block_t >

|o*arys_iterator< Key, Val, A >

|o*arys_t< Key, Val, nb, shift, mask >

|o*bad_size_exception

|o*locks::pthread::barrier

|o*counter_t::block

|o*jellyfish::capped_integer< T >

|o*jellyfish::circular_buffer< T >

|o*cite_args

|o*cite_cmdline_params

|o*cmd_func

|o*err::code

|o*concurrent_queue< Val >

|o*concurrent_queue< read_parser::reads_t >

|o*concurrent_queue< seq_qual_parser::sequence_t >

|o*concurrent_queue< sequence_parser::sequence_t >

|o*locks::pthread::cond

|o*counter_t

|o*err::die_t

|o*display_kmer

|o*divisor64

|o*jellyfish::double_fifo_input< T >

|o+jellyfish::double_fifo_input< read_parser::reads_t >

|o+jellyfish::double_fifo_input< seq_qual_parser::sequence_t >

|o+jellyfish::double_fifo_input< sequence_parser::sequence_t >

|o*dump_args

|o*dump_cmdline_params

|o*dump_fastq_main_args

|o*dump_fastq_main_cmdline_params

|o+jellyfish::dumper_t

|o*arys_t< Key, Val, nb, shift, mask >::elt

|o*ErrorWriting

|o+jellyfish::file_parser

|o*jellyfish::Float

|o*jellyfish::Float::float_int

|o*atomic::gcc

|o*generate_sequence_args

|o*generate_sequence_cmdline_params

|o*generic_list

|o*generic_value

|o*half

|o*hash_fastq_merge_args

|o*hash_fastq_merge_cmdline_params

|o*hash_merge_args

|o*hash_merge_cmdline_params

|o+jellyfish::hash_t

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >::header

|o*jellyfish::fastq_hash::header

|o*jellyfish::compacted_hash::header

|o*jellyfish::raw_hash::header

|o*jellyfish::heap_item_compare< iterator >

|o*jellyfish::heap_item_t< iterator >

|o*jellyfish::heap_t< iterator >

|o*histo_args

|o*histo_cmdline_params

|o*histo_fastq_main_args

|o*histo_fastq_main_cmdline_params

|o*jellyfish::compacted_hash::query< key_t, val_t >::iterator

|o*jellyfish::aligned_values::array< _key_t, _val_t, atomic, mem_block_t >::iterator

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >::iterator

|o*jellyfish::direct_indexing::array< key_t, val_t, atomic_t, mem_block_t >::iterator

|o*lazy_mapped_files_t

|o*locking_hash_counter< Key, Val, arys_t >

|o*allocators::malloc

|o+mapped_file

|o*mapped_files_t

|o*mer_counter_args

|o*mer_counter_cmdline_params

|o+mer_counting_base

|o*allocators::mmap

|o*locks::pthread::mutex

|o*dbg::no_flush

|o*dbg::no_print_t

|o*err::no_t

|o*jellyfish::Offsets< word >::offset_pair_t

|o*jellyfish::Offsets< word >::offset_t

|o*jellyfish::Offsets< word >

|o*jellyfish::invertible_hash::array< word, atomic_t, mem_block_t >::overlap_iterator

|o*dbg::print_t

|o*jellyfish::compacted_hash::query< key_t, val_t >

|o*jellyfish::raw_hash::query< _storage_t >

|o*query_args

|o*query_cmdline_params

|o*err::raise_t< err_t >

|o*rDNAg_t

|o*jellyfish::read_parser::read_t

|o*jellyfish::compacted_hash::reader< key_t, val_t >

|o*jellyfish::read_parser::reads_t

|o*jellyfish::invertible_hash::reprobe_limit_t

|o*locks::pthread::Semaphore

|o*jellyfish::seq_qual_parser::sequence_t

|o*jellyfish::sequence_parser::sequence_t

|o*allocators::shm

|o*jellyfish::simple_growing_array< T >

|o*SquareBinaryMatrix

|o*stats

|o*stats_args

|o*stats_cmdline_params

|o+jellyfish::storage_t

|o*dbg::str

|o*dbg::stringbuf

|o*err::substr

|o*jellyfish::parse_read::thread

|o*jellyfish::parse_quake::thread

|o*jellyfish::parse_qual_dna::thread

|o*jellyfish::hash< key_t, val_t, ary_t, atomic >::thread

|o*jellyfish::parse_dna::thread

|o+thread_exec

|o*thread_hash_counter< Key, Val, arys_t >

|o*thread_exec::thread_info

|o*jellyfish::compacted_dumper< storage_t, atomic_t >::thread_info_t

|o*jellyfish::raw_hash::dumper< storage_t >::thread_info_t

|o*jellyfish::sorted_dumper< storage_t, atomic_t >::thread_info_t

|o*jellyfish::direct_sorted_dumper< storage_t, atomic_t >::thread_info_t

|o*jellyfish::hash< key_t, val_t, ary_t, atomic >::thread_ptr_t

|o*Time

|o*allocators::mmap::tinfo

|o*token_ring< cond_t >::token

|o*token_ring< cond_t >

|o*Tptr< T >

|o*half::uif

|o*jellyfish::compacted_hash::writer< storage_t >

|o*writer_buffer

|o*writer_info

|\*dbg::xspace

o*Class Members

o*Graphical Class Hierarchy

o+Namespace List

o+File List

|o*jellyfish-1.1.2/jellyfish/aligned_values_array.hpp

|o*jellyfish-1.1.2/jellyfish/allocators_malloc.hpp

|o*jellyfish-1.1.2/jellyfish/allocators_mmap.cc

|o*jellyfish-1.1.2/jellyfish/allocators_mmap.hpp

|o*jellyfish-1.1.2/jellyfish/allocators_shm.hpp

|o*jellyfish-1.1.2/jellyfish/atomic_gcc.hpp

|o*jellyfish-1.1.2/jellyfish/backtrace.cc

|o*jellyfish-1.1.2/jellyfish/backtrace.hpp

|o*jellyfish-1.1.2/jellyfish/capped_integer.hpp

|o*jellyfish-1.1.2/jellyfish/circular_buffer.hpp

|o*jellyfish-1.1.2/jellyfish/cite.cc

|o*jellyfish-1.1.2/jellyfish/cite_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/cite_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/compacted_dumper.hpp

|o*jellyfish-1.1.2/jellyfish/compacted_hash.hpp

|o*jellyfish-1.1.2/jellyfish/concurrent_queues.hpp

|o*jellyfish-1.1.2/jellyfish/counter.hpp

|o*jellyfish-1.1.2/jellyfish/dbg.cc

|o*jellyfish-1.1.2/jellyfish/dbg.hpp

|o*jellyfish-1.1.2/jellyfish/direct_indexing_array.hpp

|o*jellyfish-1.1.2/jellyfish/direct_sorted_dumper.hpp

|o*jellyfish-1.1.2/jellyfish/divisor.hpp

|o*jellyfish-1.1.2/jellyfish/double_fifo_input.hpp

|o*jellyfish-1.1.2/jellyfish/dump_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/dump_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/dump_fastq_main.cc

|o*jellyfish-1.1.2/jellyfish/dump_fastq_main_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/dump_fastq_main_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/dump_main.cc

|o*jellyfish-1.1.2/jellyfish/dumper.hpp

|o*jellyfish-1.1.2/jellyfish/eLut.h

|o*jellyfish-1.1.2/jellyfish/err.cc

|o*jellyfish-1.1.2/jellyfish/err.hpp

|o*jellyfish-1.1.2/jellyfish/fastq_dumper.hpp

|o*jellyfish-1.1.2/jellyfish/file_parser.cc

|o*jellyfish-1.1.2/jellyfish/file_parser.hpp

|o*jellyfish-1.1.2/jellyfish/floats.cc

|o*jellyfish-1.1.2/jellyfish/floats.hpp

|o*jellyfish-1.1.2/jellyfish/generate_sequence.cc

|o*jellyfish-1.1.2/jellyfish/generate_sequence_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/generate_sequence_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/half.cpp

|o*jellyfish-1.1.2/jellyfish/half.h

|o*jellyfish-1.1.2/jellyfish/hash.hpp

|o*jellyfish-1.1.2/jellyfish/hash_fastq_merge.cc

|o*jellyfish-1.1.2/jellyfish/hash_fastq_merge_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/hash_fastq_merge_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/hash_function.hpp

|o*jellyfish-1.1.2/jellyfish/hash_merge.cc

|o*jellyfish-1.1.2/jellyfish/hash_merge_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/hash_merge_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/heap.hpp

|o*jellyfish-1.1.2/jellyfish/histo_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/histo_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/histo_fastq_main.cc

|o*jellyfish-1.1.2/jellyfish/histo_fastq_main_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/histo_fastq_main_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/histo_main.cc

|o*jellyfish-1.1.2/jellyfish/invertible_hash_array.hpp

|o*jellyfish-1.1.2/jellyfish/jellyfish.cc

|o*jellyfish-1.1.2/jellyfish/locking_hash_counters.hpp

|o*jellyfish-1.1.2/jellyfish/locks_pthread.hpp

|o*jellyfish-1.1.2/jellyfish/mapped_file.cc

|o*jellyfish-1.1.2/jellyfish/mapped_file.hpp

|o*jellyfish-1.1.2/jellyfish/mer_counter.cc

|o*jellyfish-1.1.2/jellyfish/mer_counter_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/mer_counter_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/mer_counting.hpp

|o*jellyfish-1.1.2/jellyfish/mersenne.cpp

|o*jellyfish-1.1.2/jellyfish/misc.cc

|o*jellyfish-1.1.2/jellyfish/misc.hpp

|o*jellyfish-1.1.2/jellyfish/noop_dumper.hpp

|o*jellyfish-1.1.2/jellyfish/offsets_key_value.hpp

|o*jellyfish-1.1.2/jellyfish/parse_dna.cc

|o*jellyfish-1.1.2/jellyfish/parse_dna.hpp

|o*jellyfish-1.1.2/jellyfish/parse_quake.cc

|o*jellyfish-1.1.2/jellyfish/parse_quake.hpp

|o*jellyfish-1.1.2/jellyfish/parse_qual_dna.cc

|o*jellyfish-1.1.2/jellyfish/parse_qual_dna.hpp

|o*jellyfish-1.1.2/jellyfish/parse_read.cc

|o*jellyfish-1.1.2/jellyfish/parse_read.hpp

|o*jellyfish-1.1.2/jellyfish/query_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/query_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/query_main.cc

|o*jellyfish-1.1.2/jellyfish/randomc.h

|o*jellyfish-1.1.2/jellyfish/raw_dumper.hpp

|o*jellyfish-1.1.2/jellyfish/read_parser.cc

|o*jellyfish-1.1.2/jellyfish/read_parser.hpp

|o*jellyfish-1.1.2/jellyfish/reversible_hash_function.hpp

|o*jellyfish-1.1.2/jellyfish/seq_qual_parser.cc

|o*jellyfish-1.1.2/jellyfish/seq_qual_parser.hpp

|o*jellyfish-1.1.2/jellyfish/sequence_parser.cc

|o*jellyfish-1.1.2/jellyfish/sequence_parser.hpp

|o*jellyfish-1.1.2/jellyfish/simple_growing_array.hpp

|o*jellyfish-1.1.2/jellyfish/sorted_dumper.hpp

|o*jellyfish-1.1.2/jellyfish/square_binary_matrix.cc

|o*jellyfish-1.1.2/jellyfish/square_binary_matrix.hpp

|o*jellyfish-1.1.2/jellyfish/stats_cmdline.cc

|o*jellyfish-1.1.2/jellyfish/stats_cmdline.hpp

|o*jellyfish-1.1.2/jellyfish/stats_main.cc

|o*jellyfish-1.1.2/jellyfish/storage.cc

|o*jellyfish-1.1.2/jellyfish/storage.hpp

|o*jellyfish-1.1.2/jellyfish/test_double_fifo_input.cc

|o*jellyfish-1.1.2/jellyfish/test_read_parser.cc

|o*jellyfish-1.1.2/jellyfish/thread_exec.cc

|o*jellyfish-1.1.2/jellyfish/thread_exec.hpp

|o*jellyfish-1.1.2/jellyfish/time.cc

|o*jellyfish-1.1.2/jellyfish/time.hpp

|o*jellyfish-1.1.2/jellyfish/toFloat.h

|\*jellyfish-1.1.2/jellyfish/token_ring.hpp

o+Directory Hierarchy

\*File Members