├── .clang-format ├── .gitignore ├── .gitmodules ├── .travis.yml ├── CMakeLists.txt ├── CONTRIBUTORS ├── LICENSE ├── README.md ├── cmake ├── DownloadSTXXL.cmake ├── FindSDSL.cmake ├── FindSTXXL.cmake ├── find_or_download_package.cmake ├── header_walker.cmake └── header_walker_config.json.in ├── external ├── p-clang-format │ ├── LICENSE │ ├── README.md │ └── p-clang-format └── wavelet_construction │ ├── CMakeLists.txt │ ├── IO.hpp │ ├── ddWT │ ├── CMakeLists.txt │ ├── WT.cpp │ ├── WT.hpp │ └── WTTime.cpp │ ├── ddfsWT │ ├── CMakeLists.txt │ ├── basic_wt.h │ ├── bitrank │ │ ├── basic.c │ │ ├── basic.h │ │ ├── bit_array.c │ │ ├── bit_array.h │ │ ├── bitrankw32int.c │ │ ├── bitrankw32int.h │ │ ├── del.sh │ │ └── timing.h │ ├── dd.c │ ├── util.c │ └── util.h │ ├── getmemory.hpp │ ├── levelWT │ ├── CMakeLists.txt │ ├── WT.cpp │ ├── WT.hpp │ └── WTTime.cpp │ ├── onlineWT │ ├── CMakeLists.txt │ ├── Makefile │ ├── offlineWT.cpp │ ├── onlineWT.cpp │ └── src │ │ ├── alphabet.cpp │ │ ├── alphabet.hpp │ │ ├── arrayutil.cpp │ │ ├── arrayutil.hpp │ │ ├── binheap.cpp │ │ ├── binheap.hpp │ │ ├── bitarray.cpp │ │ ├── bitarray.hpp │ │ ├── bitsandbytes.cpp │ │ ├── bitsandbytes.hpp │ │ ├── bitvector.cpp │ │ ├── bitvector.hpp │ │ ├── bytearray.cpp │ │ ├── bytearray.hpp │ │ ├── cocadautil.hpp │ │ ├── csrsbitarray.cpp │ │ ├── csrsbitarray.hpp │ │ ├── cstringutil.cpp │ │ ├── cstringutil.hpp │ │ ├── dynarray.cpp │ │ ├── dynarray.hpp │ │ ├── dynstr.cpp │ │ ├── dynstr.hpp │ │ ├── hashmap.cpp │ │ ├── hashmap.hpp │ │ ├── hashset.cpp │ │ ├── hashset.hpp │ │ ├── huffcode.cpp │ │ ├── huffcode.hpp │ │ ├── mathutil.cpp │ │ ├── mathutil.hpp │ │ ├── strstream.cpp │ │ ├── strstream.hpp │ │ ├── wavtree.cpp │ │ └── wavtree.hpp │ ├── parWT │ ├── CMakeLists.txt │ ├── basic_wt.h │ ├── bitrank │ │ ├── basic.c │ │ ├── basic.h │ │ ├── bit_array.c │ │ ├── bit_array.h │ │ ├── bitrankw32int.c │ │ ├── bitrankw32int.h │ │ ├── del.sh │ │ └── timing.h │ ├── pwt.c │ ├── util.c │ └── util.h │ ├── parallel.hpp │ ├── recWT │ ├── CMakeLists.txt │ ├── WT.cpp │ ├── WT.hpp │ └── WTTime.cpp │ ├── sdslWM │ ├── CMakeLists.txt │ ├── WT.cpp │ ├── WT.hpp │ ├── WTTime.cpp │ └── wm_int.hpp │ ├── sdslWT │ ├── CMakeLists.txt │ ├── WT.cpp │ ├── WT.hpp │ ├── WTTime.cpp │ ├── wt_int.hpp │ └── wt_pc.hpp │ ├── sequence.hpp │ ├── serialWT │ ├── CMakeLists.txt │ ├── README │ ├── WT.cpp │ ├── WT.hpp │ ├── WTTime.cpp │ └── gppDefs │ ├── sortWTOpt │ ├── CMakeLists.txt │ ├── WT.cpp │ ├── WT.hpp │ ├── WTTime.cpp │ ├── blockRadixSort.hpp │ ├── myBlockRadixSort.hpp │ └── transpose.hpp │ └── utils.hpp ├── include ├── arrays │ ├── bit_vectors.hpp │ ├── flat_two_dim_array.hpp │ ├── helper_array.hpp │ ├── memory_types.hpp │ ├── pow2_array.hpp │ └── span.hpp ├── benchmark │ ├── algorithm.hpp │ └── malloc_count.h ├── construction │ ├── building_blocks.hpp │ ├── ctx_generic.hpp │ ├── merge.hpp │ ├── pc.hpp │ ├── pc_ss.hpp │ ├── ppc.hpp │ ├── ppc_ss.hpp │ ├── pps.hpp │ ├── ps.hpp │ └── wavelet_structure.hpp ├── external_memory │ ├── full │ │ ├── dd │ │ │ ├── ctx_partial.hpp │ │ │ ├── external_dd.hpp │ │ │ ├── external_merge.hpp │ │ │ └── pc_partial.hpp │ │ └── ps │ │ │ ├── packed_io.hpp │ │ │ ├── ps_external.hpp │ │ │ ├── ps_external_packed.hpp │ │ │ └── ps_external_unpacked.hpp │ ├── internal_memory_bound.hpp │ ├── semi_in │ │ └── pc_semi_external.hpp │ ├── semi_out │ │ ├── inplace_partition.hpp │ │ ├── inplace_ps_semi_external.hpp │ │ └── ps_semi_external.hpp │ ├── stxxl_helper.hpp │ ├── wavelet_structure_external.hpp │ ├── wx_dd_pc_fe.hpp │ ├── wx_pc_ie.hpp │ ├── wx_ppc_ie.hpp │ ├── wx_ps_fe.hpp │ └── wx_ps_oe.hpp ├── huffman │ ├── README.md │ ├── ctx_huffman.hpp │ ├── huff_bit_vectors.hpp │ ├── huff_building_blocks.hpp │ ├── huff_codes.hpp │ ├── huff_dd.hpp │ ├── huff_decode.hpp │ ├── huff_level_sizes_builder.hpp │ ├── huff_merge.hpp │ ├── huff_naive.hpp │ ├── huff_parallel_level_sizes_builder.hpp │ ├── huff_pc.hpp │ ├── huff_pc_ss.hpp │ ├── huff_permutation.hpp │ └── huff_ps.hpp ├── queries │ ├── bin_rank_popcnt.hpp │ ├── bin_select_popcnt.hpp │ ├── popcnt_traits.hpp │ └── query_support.hpp ├── util │ ├── alphabet_util.hpp │ ├── bit_reverse.hpp │ ├── cacheline.hpp │ ├── common.hpp │ ├── debug.hpp │ ├── debug_assert.hpp │ ├── decode.hpp │ ├── file_util.hpp │ ├── filesystem_util.hpp │ ├── histogram.hpp │ ├── macros.hpp │ ├── meminfo.hpp │ ├── permutation.hpp │ ├── print.hpp │ ├── stats.hpp │ ├── structure_decode.hpp │ ├── type_for_bytes.hpp │ ├── uint_t.hpp │ └── uint_t │ │ └── IntegerBase.hpp ├── wx_base.hpp ├── wx_dd_pc.hpp ├── wx_dd_pc_ss.hpp ├── wx_dd_ps.hpp ├── wx_huff_dd_naive.hpp ├── wx_huff_dd_pc.hpp ├── wx_huff_dd_pc_ss.hpp ├── wx_huff_dd_ps.hpp ├── wx_huff_naive.hpp ├── wx_huff_pc.hpp ├── wx_huff_pc_ss.hpp ├── wx_huff_ps.hpp ├── wx_naive.hpp ├── wx_pc.hpp ├── wx_pc_ss.hpp ├── wx_ppc.hpp ├── wx_ppc_ss.hpp ├── wx_pps.hpp └── wx_ps.hpp ├── reducer.py ├── src ├── CMakeLists.txt ├── alphabet_count.cpp ├── benchmark.cpp ├── fastq_extract.cpp ├── malloc_count.c └── register │ ├── dd_prefix_counting.cpp │ ├── dd_prefix_counting_single_scan.cpp │ ├── dd_prefix_sorting.cpp │ ├── external_parallel_dd.cpp │ ├── external_parallel_prefix_counting.cpp │ ├── external_sequential_prefix_counting.cpp │ ├── external_sequential_prefix_sorting.cpp │ ├── huff_dd_naive.cpp │ ├── huff_dd_pc.cpp │ ├── huff_dd_pc_ss.cpp │ ├── huff_dd_ps.cpp │ ├── huff_naive.cpp │ ├── huff_pc.cpp │ ├── huff_pc_ss.cpp │ ├── huff_ps.cpp │ ├── naive.cpp │ ├── parallel_prefix_counting.cpp │ ├── parallel_prefix_counting_single_scan.cpp │ ├── parallel_prefix_sorting.cpp │ ├── sequential_prefix_counting.cpp │ ├── sequential_prefix_counting_single_scan.cpp │ └── sequential_prefix_sorting.cpp └── test ├── .gitignore ├── CMakeLists.txt ├── bin_rank_select_tests.cpp ├── bit_copy.cpp ├── construction_tests.cpp ├── huff_codes_tests.cpp ├── query_support_tests.cpp └── util ├── test_driver.cpp ├── testsuite.cmake └── util.hpp /.clang-format: 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