Full Code of nanoporetech/pod5-file-format for AI

gitextract_n9lck0re/

├── .clang-format
├── .codespellrc
├── .flake8
├── .gitattributes
├── .github/
│   └── ISSUE_TEMPLATE/
│       └── bug_report.md
├── .gitignore
├── .gitlab-ci.yml
├── .gitmodules
├── .pre-commit-config.yaml
├── .readthedocs.yaml
├── CHANGELOG.md
├── CMakeLists.txt
├── CMakePresets.json
├── DEV.md
├── LICENSE.md
├── README.md
├── benchmarks/
│   ├── .gitignore
│   ├── README.md
│   ├── build.sh
│   ├── convert/
│   │   ├── run_blow5.sh
│   │   └── run_pod5.sh
│   ├── find_all_read_ids/
│   │   ├── run_blow5.sh
│   │   ├── run_fast5.sh
│   │   └── run_pod5.sh
│   ├── find_all_samples/
│   │   ├── run_blow5.sh
│   │   ├── run_fast5.sh
│   │   └── run_pod5.sh
│   ├── find_selected_read_ids_read_number/
│   │   ├── run_blow5.sh
│   │   ├── run_fast5.sh
│   │   └── run_pod5.sh
│   ├── find_selected_read_ids_sample_count/
│   │   ├── run_blow5.sh
│   │   ├── run_fast5.sh
│   │   └── run_pod5.sh
│   ├── find_selected_read_ids_samples/
│   │   ├── run_blow5.sh
│   │   ├── run_fast5.sh
│   │   └── run_pod5.sh
│   ├── image/
│   │   ├── Dockerfile.base
│   │   ├── install_slow5.sh
│   │   └── requirements-benchmarks.txt
│   ├── run_benchmarks.py
│   ├── run_benchmarks_in_docker.sh
│   └── tools/
│       ├── check_csvs_consistent.py
│       ├── fast5_to_single_blow5.sh
│       ├── find_and_get_fast5.py
│       ├── find_and_get_pod5.py
│       ├── pyslow5_tests.py
│       ├── run_benchmarks_docker_entry.sh
│       └── select-random-ids.py
├── c++/
│   ├── CMakeLists.txt
│   ├── examples/
│   │   ├── CMakeLists.txt
│   │   ├── README.md
│   │   ├── find_all_read_data.cpp
│   │   ├── find_all_read_ids.cpp
│   │   ├── find_specific_read_ids.cpp
│   │   └── find_specific_read_ids_with_signal.cpp
│   ├── pod5_format/
│   │   ├── async_signal_loader.cpp
│   │   ├── async_signal_loader.h
│   │   ├── c_api.cpp
│   │   ├── c_api.h
│   │   ├── dictionary_writer.h
│   │   ├── expandable_buffer.h
│   │   ├── file_output_stream.h
│   │   ├── file_reader.cpp
│   │   ├── file_reader.h
│   │   ├── file_recovery.h
│   │   ├── file_updater.cpp
│   │   ├── file_updater.h
│   │   ├── file_writer.cpp
│   │   ├── file_writer.h
│   │   ├── flatbuffers/
│   │   │   └── footer.fbs
│   │   ├── internal/
│   │   │   ├── async_output_stream.h
│   │   │   ├── combined_file_utils.h
│   │   │   ├── linux_output_stream.h
│   │   │   └── tracing/
│   │   │       └── tracing.h
│   │   ├── io_manager.cpp
│   │   ├── io_manager.h
│   │   ├── memory_pool.cpp
│   │   ├── memory_pool.h
│   │   ├── migration/
│   │   │   ├── migration.cpp
│   │   │   ├── migration.h
│   │   │   ├── migration_utils.h
│   │   │   ├── v0_to_v1.cpp
│   │   │   ├── v1_to_v2.cpp
│   │   │   ├── v2_to_v3.cpp
│   │   │   └── v3_to_v4.cpp
│   │   ├── read_table_reader.cpp
│   │   ├── read_table_reader.h
│   │   ├── read_table_schema.cpp
│   │   ├── read_table_schema.h
│   │   ├── read_table_utils.cpp
│   │   ├── read_table_utils.h
│   │   ├── read_table_writer.cpp
│   │   ├── read_table_writer.h
│   │   ├── read_table_writer_utils.cpp
│   │   ├── read_table_writer_utils.h
│   │   ├── result.h
│   │   ├── run_info_table_reader.cpp
│   │   ├── run_info_table_reader.h
│   │   ├── run_info_table_schema.cpp
│   │   ├── run_info_table_schema.h
│   │   ├── run_info_table_writer.cpp
│   │   ├── run_info_table_writer.h
│   │   ├── schema_field_builder.h
│   │   ├── schema_metadata.cpp
│   │   ├── schema_metadata.h
│   │   ├── schema_utils.cpp
│   │   ├── schema_utils.h
│   │   ├── signal_builder.h
│   │   ├── signal_compression.cpp
│   │   ├── signal_compression.h
│   │   ├── signal_table_reader.cpp
│   │   ├── signal_table_reader.h
│   │   ├── signal_table_schema.cpp
│   │   ├── signal_table_schema.h
│   │   ├── signal_table_utils.h
│   │   ├── signal_table_writer.cpp
│   │   ├── signal_table_writer.h
│   │   ├── svb16/
│   │   │   ├── common.hpp
│   │   │   ├── decode.hpp
│   │   │   ├── decode_scalar.hpp
│   │   │   ├── decode_x64.hpp
│   │   │   ├── encode.hpp
│   │   │   ├── encode_scalar.hpp
│   │   │   ├── encode_x64.hpp
│   │   │   ├── generate_shuffle_tables.py
│   │   │   ├── intrinsics.hpp
│   │   │   ├── shuffle_tables.hpp
│   │   │   ├── simd_detect_x64.hpp
│   │   │   ├── streamvbytedelta_decode_16.c
│   │   │   ├── streamvbytedelta_encode_16.c
│   │   │   ├── streamvbytedelta_x64_decode_16.c
│   │   │   ├── streamvbytedelta_x64_encode_16.c
│   │   │   ├── svb16.c
│   │   │   └── svb16.h
│   │   ├── table_reader.cpp
│   │   ├── table_reader.h
│   │   ├── thread_pool.cpp
│   │   ├── thread_pool.h
│   │   ├── tuple_utils.h
│   │   ├── types.cpp
│   │   ├── types.h
│   │   ├── uuid.h
│   │   └── version.h.in
│   ├── pod5_format_pybind/
│   │   ├── CMakeLists.txt
│   │   ├── _version.py.in
│   │   ├── api.h
│   │   ├── bindings.cpp
│   │   ├── build_wheel.cmake
│   │   ├── repack/
│   │   │   ├── repack_functions.h
│   │   │   ├── repack_output.cpp
│   │   │   ├── repack_output.h
│   │   │   ├── repack_states.h
│   │   │   ├── repack_utils.h
│   │   │   ├── repacker.cpp
│   │   │   └── repacker.h
│   │   ├── subset.cpp
│   │   ├── subset.h
│   │   └── utils.h
│   └── test/
│       ├── CMakeLists.txt
│       ├── TemporaryDirectory.h
│       ├── c_api_build_test.c
│       ├── c_api_null_input.cpp
│       ├── c_api_test_utils.h
│       ├── c_api_tests.cpp
│       ├── file_reader_writer_tests.cpp
│       ├── main.cpp
│       ├── output_stream_tests.cpp
│       ├── read_table_tests.cpp
│       ├── read_table_writer_utils_tests.cpp
│       ├── run_info_table_tests.cpp
│       ├── schema_tests.cpp
│       ├── signal_compression_tests.cpp
│       ├── signal_table_tests.cpp
│       ├── svb16_scalar_tests.cpp
│       ├── svb16_x64_tests.cpp
│       ├── test_utils.h
│       ├── thread_pool_tests.cpp
│       ├── utils.h
│       └── uuid_tests.cpp
├── ci/
│   ├── docker/
│   │   ├── Dockerfile.conda
│   │   ├── Dockerfile.py39.arm64
│   │   └── Dockerfile.py39.x64
│   ├── generate_coverage_report.sh
│   ├── get_tag_version.cmake
│   ├── gitlab-ci-common.yml
│   ├── install.sh
│   ├── package.sh
│   └── unpack_libs_for_python.sh
├── cmake/
│   ├── BuildFlatBuffers.cmake
│   ├── Findzstd.cmake
│   ├── conan_provider.cmake
│   ├── pod5_fuzz.cmake
│   ├── pod5_packaging.cmake
│   └── presets/
│       ├── conan-build-options.json
│       ├── conan-profiles.json
│       └── conan-provider.json
├── conanfile.py
├── docs/
│   ├── DESIGN.md
│   ├── README.md
│   ├── SPECIFICATION.md
│   └── tables/
│       ├── reads.toml
│       ├── run_info.toml
│       └── signal.toml
├── fuzz/
│   ├── .gitattributes
│   ├── CMakeLists.txt
│   ├── fuzz_compress.cpp
│   ├── fuzz_file.cpp
│   └── runner.cpp
├── pod5_make_version.py
├── pyproject.toml
├── pytest.ini
├── python/
│   ├── .gitignore
│   ├── lib_pod5/
│   │   ├── Makefile
│   │   ├── README.md
│   │   ├── pyproject.toml
│   │   ├── setup.py
│   │   └── src/
│   │       ├── lib_pod5/
│   │       │   ├── __init__.py
│   │       │   ├── pod5_format_pybind.pyi
│   │       │   └── py.typed
│   │       └── test/
│   │           └── test_lib_pod5.py
│   └── pod5/
│       ├── Makefile
│       ├── README.md
│       ├── examples/
│       │   ├── find_all_reads.py
│       │   └── find_specific_reads.py
│       ├── pyproject.toml
│       ├── setup.py
│       ├── src/
│       │   ├── pod5/
│       │   │   ├── __init__.py
│       │   │   ├── api_utils.py
│       │   │   ├── dataset.py
│       │   │   ├── pod5_types.py
│       │   │   ├── reader.py
│       │   │   ├── repack.py
│       │   │   ├── signal_tools.py
│       │   │   ├── tools/
│       │   │   │   ├── __init__.py
│       │   │   │   ├── main.py
│       │   │   │   ├── parsers.py
│       │   │   │   ├── pod5_convert_from_fast5.py
│       │   │   │   ├── pod5_convert_to_fast5.py
│       │   │   │   ├── pod5_filter.py
│       │   │   │   ├── pod5_inspect.py
│       │   │   │   ├── pod5_merge.py
│       │   │   │   ├── pod5_recover.py
│       │   │   │   ├── pod5_repack.py
│       │   │   │   ├── pod5_subset.py
│       │   │   │   ├── pod5_update.py
│       │   │   │   ├── pod5_view.py
│       │   │   │   ├── polars_utils.py
│       │   │   │   └── utils.py
│       │   │   └── writer.py
│       │   └── tests/
│       │       ├── __init__.py
│       │       ├── conftest.py
│       │       ├── test_api.py
│       │       ├── test_convert_from_fast5.py
│       │       ├── test_convert_to_fast5.py
│       │       ├── test_dataset.py
│       │       ├── test_filter.py
│       │       ├── test_inspect.py
│       │       ├── test_merge.py
│       │       ├── test_reader.py
│       │       ├── test_recover.py
│       │       ├── test_repack.py
│       │       ├── test_signal_tools.py
│       │       ├── test_subset.py
│       │       ├── test_tools.py
│       │       ├── test_update.py
│       │       ├── test_view.py
│       │       └── test_writer.py
│       └── test_utils/
│           └── check_pod5_files_equal.py
├── test_data/
│   ├── multi_fast5_zip.fast5
│   ├── multi_fast5_zip_v0.pod5
│   ├── multi_fast5_zip_v1.pod5
│   ├── multi_fast5_zip_v2.pod5
│   ├── multi_fast5_zip_v3.pod5
│   ├── multi_fast5_zip_v4.pod5
│   ├── single_read_fast5/
│   │   └── fe85b517-62ee-4a33-8767-41cab5d5ab39.fast5.single-read
│   ├── split_1_v4.pod5
│   ├── split_2_v4.pod5
│   └── subset_mapping_examples/
│       ├── read_ids.txt
│       ├── subset.csv
│       └── subset.summary
├── test_package/
│   ├── CMakeLists.txt
│   ├── conanfile.py
│   ├── test_cpp_api.cpp
│   └── test_package.cpp
└── third_party/
    ├── build_instructions.txt
    ├── gsl-disable-gsl-suppress.patch
    ├── include/
    │   ├── .editorconfig
    │   ├── catch2/
    │   │   └── catch.hpp
    │   ├── gsl/
    │   │   ├── gsl
    │   │   ├── gsl-lite-vc6.hpp
    │   │   ├── gsl-lite.h
    │   │   └── gsl-lite.hpp
    │   └── gsl.h
    ├── jsoncons-0.166-icc-fix.patch
    ├── licenses/
    │   ├── catch2.txt
    │   └── gsl-lite.txt
    └── software_versions.yaml

SYMBOL INDEX (3153 symbols across 168 files)

FILE: benchmarks/run_benchmarks.py
  function du (line 33) | def du(path):
  function generate_report (line 38) | def generate_report(input_dir, output_dir, timing_results):
  function check_read_ids (line 89) | def check_read_ids(benchmark, file_types, output_dir, only_format):
  function check_file_sizes (line 104) | def check_file_sizes(benchmark, file_types, output_dir, only_format):
  function copy_fast5_files (line 109) | def copy_fast5_files(benchmark, input_dir, output_dir):
  function randomly_select_read_ids (line 113) | def randomly_select_read_ids(benchmark, input_dir, output_dir):
  function run_benchmark (line 188) | def run_benchmark(benchmark, input_dir, output_dir, only_format=None):
  function run_benchmarks (line 234) | def run_benchmarks(args):
  function main (line 274) | def main():

FILE: benchmarks/tools/check_csvs_consistent.py
  function check_consistency (line 10) | def check_consistency(df1, df2):
  function main (line 20) | def main():

FILE: benchmarks/tools/find_and_get_fast5.py
  function select_reads (line 11) | def select_reads(file, selection):
  function run (line 24) | def run(input_dir, output, select_read_ids=None, get_columns=[]):
  function main (line 60) | def main():

FILE: benchmarks/tools/find_and_get_pod5.py
  function load_mapped_ids (line 20) | def load_mapped_ids(select_read_ids_data):
  function do_batch_work (line 33) | def do_batch_work(filename, batches, column, mode, result_q):
  function do_search_work (line 54) | def do_search_work(files, select_read_ids_data, column, mode, result_q):
  function run_multiprocess (line 75) | def run_multiprocess(files, output, select_read_ids=None, column=None, m...
  function run_get_read_ids (line 151) | def run_get_read_ids(files):
  function run_select (line 163) | def run_select(files, select_read_ids, column):
  function run_batched (line 190) | def run_batched(files, column):
  function main (line 213) | def main():

FILE: benchmarks/tools/pyslow5_tests.py
  function random_access (line 13) | def random_access(s5_file, read_list, col, result_q):
  function run (line 37) | def run(s5_file, benchmark, select_read_ids, col):
  function main (line 103) | def main():

FILE: benchmarks/tools/select-random-ids.py
  function main (line 9) | def main():

FILE: c++/examples/find_all_read_data.cpp
  function main (line 9) | int main(int argc, char ** argv)

FILE: c++/examples/find_all_read_ids.cpp
  function main (line 9) | int main(int argc, char ** argv)

FILE: c++/examples/find_specific_read_ids.cpp
  function main (line 8) | int main(int argc, char ** argv)

FILE: c++/examples/find_specific_read_ids_with_signal.cpp
  function main (line 8) | int main(int argc, char ** argv)

FILE: c++/pod5_format/async_signal_loader.cpp
  type pod5 (line 3) | namespace pod5 {
    function Status (line 230) | Status AsyncSignalLoader::setup_next_in_progress_batch(std::unique_loc...

FILE: c++/pod5_format/async_signal_loader.h
  function namespace (line 18) | namespace pod5 {
  function complete_rows (line 96) | void complete_rows(std::uint32_t row_count) { m_completed_rows += row_co...
  function class (line 113) | class POD5_FORMAT_EXPORT AsyncSignalLoader {

FILE: c++/pod5_format/c_api.cpp
  type Pod5FileReader (line 21) | struct Pod5FileReader {
    method Pod5FileReader (line 22) | Pod5FileReader(std::shared_ptr<pod5::FileReader> && reader_) : reader(...
  type Pod5FileWriter (line 27) | struct Pod5FileWriter {
    method Pod5FileWriter (line 28) | Pod5FileWriter(std::unique_ptr<pod5::FileWriter> && writer_) : writer(...
  type Pod5ReadRecordBatch (line 33) | struct Pod5ReadRecordBatch {
    method Pod5ReadRecordBatch (line 34) | Pod5ReadRecordBatch(
  function pod5_set_error (line 51) | void pod5_set_error(arrow::Status status)
  function pod5_reset_error (line 57) | void pod5_reset_error()
  function check_string_not_empty (line 85) | bool check_string_not_empty(char const * str)
  function check_not_null (line 100) | bool check_not_null(void const * ptr)
  function check_file_not_null (line 109) | bool check_file_not_null(void const * file)
  function check_output_pointer_not_null (line 118) | bool check_output_pointer_not_null(void const * output)
  function make_internal_writer_options (line 128) | pod5::FileWriterOptions make_internal_writer_options(Pod5WriterOptions c...
  function make_internal_reader_options (line 150) | pod5::FileReaderOptions make_internal_reader_options(Pod5ReaderOptions c...
  function pod5_error_t (line 162) | pod5_error_t pod5_init()
  function pod5_error_t (line 169) | pod5_error_t pod5_terminate()
  function pod5_error_t (line 176) | pod5_error_t pod5_get_error_no() { return g_pod5_error_no; }
  function Pod5FileReader (line 181) | Pod5FileReader * pod5_open_file(char const * filename)
    method Pod5FileReader (line 22) | Pod5FileReader(std::shared_ptr<pod5::FileReader> && reader_) : reader(...
  function Pod5FileReader (line 187) | Pod5FileReader * pod5_open_file_options(char const * filename, Pod5Reade...
    method Pod5FileReader (line 22) | Pod5FileReader(std::shared_ptr<pod5::FileReader> && reader_) : reader(...
  function pod5_error_t (line 205) | pod5_error_t pod5_close_and_free_reader(Pod5FileReader * file)
  function pod5_error_t (line 214) | pod5_error_t pod5_get_file_info(Pod5FileReader_t const * reader, FileInf...
  function pod5_error_t (line 232) | pod5_error_t pod5_get_file_read_table_location(
  function pod5_error_t (line 249) | pod5_error_t pod5_get_file_signal_table_location(
  function pod5_error_t (line 266) | pod5_error_t pod5_get_file_run_info_table_location(
  function pod5_error_t (line 283) | pod5_error_t pod5_get_read_count(Pod5FileReader_t const * reader, size_t...
  function pod5_error_t (line 296) | pod5_error_t pod5_get_read_ids(Pod5FileReader_t const * reader, size_t c...
  function pod5_error_t (line 326) | pod5_error_t pod5_plan_traversal(
  function pod5_error_t (line 360) | pod5_error_t pod5_get_read_batch_count(size_t * count, Pod5FileReader co...
  function pod5_error_t (line 372) | pod5_error_t
  function pod5_error_t (line 390) | pod5_error_t pod5_free_read_batch(Pod5ReadRecordBatch * batch)
  function pod5_error_t (line 399) | pod5_error_t pod5_get_read_batch_row_count(size_t * count, Pod5ReadRecor...
  function pod5_error_t (line 411) | static pod5_error_t check_row_index_and_set_error(size_t row, int64_t ba...
  function pod5_error_t (line 425) | pod5_error_t pod5_get_read_batch_row_info_data(
  function pod5_error_t (line 517) | pod5_error_t pod5_get_signal_row_indices(
  function pod5_error_t (line 554) | pod5_error_t pod5_get_calibration_extra_info(
  type RunInfoDataCHelper (line 588) | struct RunInfoDataCHelper : public RunInfoDictData {
    type InternalMapHelper (line 589) | struct InternalMapHelper {
    method RunInfoDataCHelper (line 594) | RunInfoDataCHelper(std::shared_ptr<pod5::RunInfoData const> && interna...
    method KeyValueData (line 619) | KeyValueData map_to_c(pod5::RunInfoData::MapType const & map, Internal...
  function pod5_error_t (line 642) | pod5_error_t pod5_get_run_info(
  function pod5_error_t (line 661) | pod5_error_t pod5_get_file_run_info(
  function pod5_error_t (line 679) | pod5_error_t pod5_free_run_info(RunInfoDictData_t * run_info_data)
  function pod5_error_t (line 689) | pod5_error_t pod5_release_run_info(RunInfoDictData * run_info_data)
  function pod5_error_t (line 694) | pod5_error_t pod5_get_file_run_info_count(
  function pod5_error_t (line 709) | pod5_error_t pod5_get_end_reason(
  function pod5_error_t (line 771) | pod5_error_t pod5_get_pore_type(
  class SignalRowInfoCHelper (line 799) | class SignalRowInfoCHelper : public SignalRowInfo {
    method SignalRowInfoCHelper (line 801) | SignalRowInfoCHelper(pod5::SignalTableRecordBatch && b) : batch(std::m...
  function pod5_error_t (line 808) | pod5_error_t pod5_get_signal_row_info(
  function pod5_error_t (line 868) | pod5_error_t pod5_free_signal_row_info(size_t signal_rows_count, SignalR...
  function pod5_error_t (line 884) | pod5_error_t pod5_get_signal(
  function pod5_error_t (line 906) | pod5_error_t pod5_get_read_complete_sample_count(
  function pod5_error_t (line 929) | pod5_error_t pod5_get_read_complete_signal(
  function Pod5FileWriter (line 953) | Pod5FileWriter *
    method Pod5FileWriter (line 28) | Pod5FileWriter(std::unique_ptr<pod5::FileWriter> && writer_) : writer(...
  function pod5_error_t (line 973) | pod5_error_t pod5_close_and_free_writer(Pod5FileWriter * file)
  function pod5_error_t (line 986) | pod5_error_t pod5_add_pore(int16_t * pore_index, Pod5FileWriter * file, ...
  function pod5_error_t (line 1000) | pod5_error_t pod5_add_run_info(
  function check_read_data_struct (line 1097) | static bool check_read_data_struct(std::uint16_t struct_version, void co...
  function load_struct_row_into_read_data (line 1154) | static bool load_struct_row_into_read_data(
  function pod5_error_t (line 1266) | pod5_error_t pod5_add_reads_data(
  function pod5_error_t (line 1308) | pod5_error_t pod5_add_reads_data_pre_compressed(
  function pod5_vbz_compressed_signal_max_size (line 1371) | size_t pod5_vbz_compressed_signal_max_size(size_t sample_count)
  function pod5_error_t (line 1385) | pod5_error_t pod5_vbz_compress_signal(
  function pod5_error_t (line 1420) | pod5_error_t pod5_vbz_decompress_signal(
  function pod5_error_t (line 1440) | pod5_error_t pod5_format_read_id(read_id_t const read_id, char * read_id...

FILE: c++/pod5_format/c_api.h
  type Pod5FileReader (line 23) | struct Pod5FileReader
  type Pod5FileReader_t (line 24) | typedef struct Pod5FileReader Pod5FileReader_t;
  type Pod5FileWriter (line 25) | struct Pod5FileWriter
  type Pod5FileWriter_t (line 26) | typedef struct Pod5FileWriter Pod5FileWriter_t;
  type Pod5ReadRecordBatch (line 27) | struct Pod5ReadRecordBatch
  type Pod5ReadRecordBatch_t (line 28) | typedef struct Pod5ReadRecordBatch Pod5ReadRecordBatch_t;
  type pod5_error (line 36) | enum pod5_error {
  type pod5_error_t (line 51) | typedef enum pod5_error pod5_error_t;
  type pod5_end_reason (line 72) | enum pod5_end_reason {
  type pod5_end_reason_t (line 84) | typedef enum pod5_end_reason pod5_end_reason_t;
  type run_info_index_t (line 86) | typedef uint16_t run_info_index_t;
  type ReadBatchRowInfoV3 (line 92) | struct ReadBatchRowInfoV3 {
  type ReadBatchRowInfoV4 (line 148) | struct ReadBatchRowInfoV4 {
  type ReadBatchRowInfo_t (line 207) | typedef struct ReadBatchRowInfoV4 ReadBatchRowInfo_t;
  function ReadBatchRowInfoArrayV3 (line 209) | struct POD5_DEPRECATED ReadBatchRowInfoArrayV3 {
  type ReadBatchRowInfoArrayV4 (line 259) | struct ReadBatchRowInfoArrayV4 {
  type ReadBatchRowInfoArray_t (line 312) | typedef struct ReadBatchRowInfoArrayV4 ReadBatchRowInfoArray_t;
  type Pod5ReaderOptions (line 331) | struct Pod5ReaderOptions {
  type Pod5ReaderOptions_t (line 336) | typedef struct Pod5ReaderOptions Pod5ReaderOptions_t;
  type FileInfo (line 358) | struct FileInfo {
  type FileInfo_t (line 367) | typedef struct FileInfo FileInfo_t;
  type EmbeddedFileData (line 375) | struct EmbeddedFileData {
  type EmbeddedFileData_t (line 382) | typedef struct EmbeddedFileData EmbeddedFileData_t;
  type CalibrationExtraData (line 489) | struct CalibrationExtraData {
  type CalibrationExtraData_t (line 497) | typedef struct CalibrationExtraData CalibrationExtraData_t;
  type KeyValueData (line 509) | struct KeyValueData {
  type RunInfoDictData (line 515) | struct RunInfoDictData {
  type RunInfoDictData_t (line 537) | typedef struct RunInfoDictData RunInfoDictData_t;
  type SignalRowInfo (line 602) | struct SignalRowInfo {
  type SignalRowInfo_t (line 608) | typedef struct SignalRowInfo SignalRowInfo_t;
  type CompressionOption (line 671) | enum CompressionOption {
  type Pod5WriterOptions (line 681) | struct Pod5WriterOptions {
  type Pod5WriterOptions_t (line 694) | typedef struct Pod5WriterOptions Pod5WriterOptions_t;

FILE: c++/pod5_format/dictionary_writer.h
  function namespace (line 6) | namespace arrow {
  function namespace (line 10) | namespace pod5 {

FILE: c++/pod5_format/expandable_buffer.h
  function namespace (line 9) | namespace pod5 {

FILE: c++/pod5_format/file_output_stream.h
  function namespace (line 6) | namespace pod5 {

FILE: c++/pod5_format/file_reader.cpp
  type pod5 (line 20) | namespace pod5 {
    function warn_if_stat_size_and_blocks_differ_significantly (line 28) | void warn_if_stat_size_and_blocks_differ_significantly(std::string con...
    function warn_if_stat_size_and_blocks_differ_significantly (line 58) | void warn_if_stat_size_and_blocks_differ_significantly(std::string con...
    function FileLocation (line 74) | inline FileLocation make_file_locaton(combined_file_utils::ParsedFileI...
    class FileReaderImpl (line 82) | class FileReaderImpl : public FileReader {
      method FileReaderImpl (line 84) | FileReaderImpl(
      method SchemaMetadataDescription (line 101) | SchemaMetadataDescription schema_metadata() const override
      method run_info_count (line 106) | Result<std::size_t> run_info_count() const override
      method read_count (line 111) | virtual Result<std::size_t> read_count() const override
      method read_read_record_batch (line 124) | Result<ReadTableRecordBatch> read_read_record_batch(std::size_t i) c...
      method num_read_record_batches (line 129) | std::size_t num_read_record_batches() const override
      method search_for_read_ids (line 134) | Result<std::size_t> search_for_read_ids(
      method read_signal_record_batch (line 142) | Result<SignalTableRecordBatch> read_signal_record_batch(std::size_t ...
      method num_signal_record_batches (line 147) | std::size_t num_signal_record_batches() const override
      method signal_batch_for_row_id (line 152) | Result<std::size_t> signal_batch_for_row_id(std::size_t row, std::si...
      method extract_sample_count (line 158) | Result<std::size_t> extract_sample_count(
      method Status (line 164) | Status extract_samples(
      method extract_samples_inplace (line 171) | Result<std::vector<std::shared_ptr<arrow::Buffer>>> extract_samples_...
      method FileLocation (line 178) | FileLocation const & run_info_table_location() const override
      method FileLocation (line 183) | FileLocation const & read_table_location() const override { return m...
      method FileLocation (line 185) | FileLocation const & signal_table_location() const override { return...
      method Version (line 187) | Version file_version_pre_migration() const override { return m_file_...
      method SignalType (line 189) | SignalType signal_type() const override { return m_signal_table_read...
      method find_run_info (line 191) | Result<std::shared_ptr<RunInfoData const>> find_run_info(
      method get_run_info (line 197) | Result<std::shared_ptr<RunInfoData const>> get_run_info(std::size_t ...
      method get_run_info_count (line 202) | Result<std::size_t> get_run_info_count() const override
    function open_file_reader (line 218) | pod5::Result<std::shared_ptr<FileReader>> open_file_reader(

FILE: c++/pod5_format/file_reader.h
  function namespace (line 11) | namespace arrow {
  function namespace (line 17) | namespace pod5 {

FILE: c++/pod5_format/file_recovery.h
  function namespace (line 13) | namespace pod5 {

FILE: c++/pod5_format/file_updater.cpp
  type pod5 (line 10) | namespace pod5 {
    function update_file (line 12) | pod5::Status update_file(

FILE: c++/pod5_format/file_updater.h
  function namespace (line 7) | namespace arrow {
  function namespace (line 11) | namespace pod5 {

FILE: c++/pod5_format/file_writer.cpp
  type CachedFileValues (line 33) | struct CachedFileValues {
  type FlushMode (line 38) | enum class FlushMode { Default, ForceFlushOnBatchComplete }
  function make_file_stream (line 40) | arrow::Result<std::shared_ptr<pod5::FileOutputStream>> make_file_stream(
  type pod5 (line 93) | namespace pod5 {
    class FileWriterImpl (line 112) | class FileWriterImpl {
      class WriterTypeImpl (line 114) | class WriterTypeImpl
      type DictionaryWriters (line 116) | struct DictionaryWriters {
      method FileWriterImpl (line 122) | FileWriterImpl(
      method lookup_end_reason (line 142) | pod5::Result<EndReasonDictionaryIndex> lookup_end_reason(ReadEndReas...
      method add_pore_type (line 147) | pod5::Result<PoreDictionaryIndex> add_pore_type(std::string const & ...
      method add_run_info (line 152) | pod5::Result<RunInfoDictionaryIndex> add_run_info(RunInfoData const ...
      method add_complete_read (line 158) | pod5::Status add_complete_read(
      method add_complete_read (line 177) | pod5::Status add_complete_read(
      method check_read (line 194) | arrow::Status check_read(ReadData const & read_data)
      method add_signal (line 211) | pod5::Result<std::vector<SignalTableRowIndex>> add_signal(
      method add_pre_compressed_signal (line 238) | pod5::Result<SignalTableRowIndex> add_pre_compressed_signal(
      method add_signal_batch (line 251) | pod5::Result<std::pair<SignalTableRowIndex, SignalTableRowIndex>> ad...
      method SignalType (line 263) | SignalType signal_type() const { return m_signal_table_writer->signa...
      method signal_table_batch_size (line 265) | std::size_t signal_table_batch_size() const
      method close_run_info_table_writer (line 270) | pod5::Status close_run_info_table_writer()
      method close_read_table_writer (line 279) | pod5::Status close_read_table_writer()
      method close_signal_table_writer (line 288) | pod5::Status close_signal_table_writer()
      method is_closed (line 299) | bool is_closed() const
      method RunInfoTableWriter (line 307) | RunInfoTableWriter * run_info_table_writer()
      method ReadTableWriter (line 315) | ReadTableWriter * read_table_writer()
      method SignalTableWriter (line 323) | SignalTableWriter * signal_table_writer()
    class CombinedFileWriterImpl (line 340) | class CombinedFileWriterImpl : public FileWriterImpl {
      method CombinedFileWriterImpl (line 342) | CombinedFileWriterImpl(
      method path (line 373) | std::string path() const override { return m_path; }
      method close (line 375) | arrow::Status close() override
    function SignalType (line 511) | SignalType FileWriter::signal_type() const { return m_impl->signal_typ...
    function make_dictionary_writers (line 518) | pod5::Result<FileWriterImpl::DictionaryWriters> make_dictionary_writer...
    function make_reads_tmp_path (line 529) | std::string make_reads_tmp_path(
    function make_run_info_tmp_path (line 536) | std::string make_run_info_tmp_path(
    function create_file_writer (line 544) | pod5::Result<std::unique_ptr<FileWriter>> create_file_writer(
    function Status (line 655) | static Status add_recovery_failure_context(
    function Status (line 670) | static Status append_recovered_file(
    type TemporaryFilePaths (line 693) | struct TemporaryFilePaths {
    function recover_file (line 699) | static pod5::Status recover_file(
    function is_useless (line 779) | static bool is_useless(std::filesystem::path const & file_path)
    function remove_if_useless (line 801) | static void remove_if_useless(std::filesystem::path const & file_path)
    function try_remove (line 808) | static std::optional<CleanupError> try_remove(std::string const & file...
    function Status (line 818) | static Status add_clean_up_error(Status status, std::filesystem::files...
    function recover_file (line 823) | pod5::Result<RecoveryDetails> recover_file(

FILE: c++/pod5_format/file_writer.h
  function namespace (line 11) | namespace arrow {
  function namespace (line 16) | namespace pod5 {

FILE: c++/pod5_format/internal/async_output_stream.h
  type PrivateDummy (line 19) | struct PrivateDummy {}
  function override (line 70) | const override
  function set_file_start_offset (line 162) | void set_file_start_offset(std::size_t val) override { m_file_start_offs...
  function FILE (line 205) | FILE * get_or_open_file_handle([[maybe_unused]] std::lock_guard<std::mut...
  function close_file_handle (line 215) | void close_file_handle([[maybe_unused]] std::lock_guard<std::mutex> & lock)
  function set_error (line 223) | void set_error(arrow::Status status)
  function FILE (line 253) | FILE * m_file_handle{nullptr};

FILE: c++/pod5_format/internal/combined_file_utils.h
  function pod5 (line 24) | inline pod5::Status pad_file(
  function pod5 (line 38) | inline pod5::Status write_file_signature(std::shared_ptr<arrow::io::Outp...
  function pod5 (line 43) | inline pod5::Status write_section_marker(
  function pod5 (line 50) | inline pod5::Status write_combined_header(
  function pod5 (line 58) | inline pod5::Status write_footer_magic(std::shared_ptr<arrow::io::Output...
  type FileInfo (line 63) | struct FileInfo {
  function FileInfo (line 68) | struct ParsedFileInfo : FileInfo {
  function pod5 (line 83) | inline pod5::Result<std::int64_t> write_footer_flatbuffer(
  function arrow (line 365) | inline arrow::Result<std::shared_ptr<SubFile>> open_sub_file(ParsedFileI...
  function arrow (line 383) | inline arrow::Result<std::shared_ptr<SubFile>> open_sub_file(
  function SubFileCleanup (line 399) | enum class SubFileCleanup { CleanupOriginalFile, LeaveOrignalFile };

FILE: c++/pod5_format/internal/linux_output_stream.h
  function namespace (line 19) | namespace pod5 {

FILE: c++/pod5_format/io_manager.cpp
  type pod5 (line 7) | namespace pod5 {
    class IOManagerSyncImpl (line 10) | class IOManagerSyncImpl : public IOManager {
      method IOManagerSyncImpl (line 12) | IOManagerSyncImpl(arrow::MemoryPool * memory_pool) : m_memory_pool(m...
      method allocate_new_write (line 14) | arrow::Result<std::shared_ptr<QueuedWrite>> allocate_new_write(std::...
      method return_used_write (line 34) | arrow::Status return_used_write(std::shared_ptr<QueuedWrite> && used...
      method write_buffer (line 43) | arrow::Status write_buffer(std::shared_ptr<QueuedWrite> && data) ove...
    function make_sync_io_manager (line 74) | arrow::Result<std::shared_ptr<IOManager>> make_sync_io_manager(arrow::...

FILE: c++/pod5_format/io_manager.h
  function prepare_for_write (line 36) | void prepare_for_write(int file_descriptor, std::uint64_t offset)
  function iovec (line 52) | iovec * get_iovec_for_buffer() { return &m_iovec; }
  type class (line 54) | enum class
  function set_state (line 58) | void set_state(WriteState state) { m_state = state; }
  function iovec (line 63) | iovec m_iovec{}
  function m_file_descriptor (line 64) | int m_file_descriptor{-1};

FILE: c++/pod5_format/memory_pool.cpp
  function os_page_detect (line 13) | size_t os_page_detect(void)
  type pod5 (line 36) | namespace pod5 {

FILE: c++/pod5_format/memory_pool.h
  function namespace (line 4) | namespace pod5 {

FILE: c++/pod5_format/migration/migration.cpp
  type pod5 (line 5) | namespace pod5 {
    function register_delete_at_exit (line 10) | void register_delete_at_exit(arrow::internal::PlatformFilename const &...
    function MakeTmpDir (line 33) | Result<std::unique_ptr<TemporaryDir>> MakeTmpDir(char const * suffix)

FILE: c++/pod5_format/migration/migration.h
  function namespace (line 11) | namespace pod5 {

FILE: c++/pod5_format/migration/migration_utils.h
  function namespace (line 14) | namespace pod5 {

FILE: c++/pod5_format/migration/v0_to_v1.cpp
  type pod5 (line 11) | namespace pod5 {
    function migrate_v0_to_v1 (line 13) | arrow::Result<MigrationResult> migrate_v0_to_v1(

FILE: c++/pod5_format/migration/v1_to_v2.cpp
  type pod5 (line 12) | namespace pod5 {
    function get_num_samples (line 14) | arrow::Result<std::size_t> get_num_samples(
    function migrate_v1_to_v2 (line 65) | arrow::Result<MigrationResult> migrate_v1_to_v2(

FILE: c++/pod5_format/migration/v2_to_v3.cpp
  type pod5 (line 13) | namespace pod5 {
    type StructRow (line 15) | struct StructRow {
    type StringDictBuilder (line 20) | struct StringDictBuilder {
      method finish (line 24) | arrow::Result<std::shared_ptr<arrow::Array>> finish()
    function get_dict_struct (line 42) | arrow::Result<StructRow> get_dict_struct(
    function append_struct_row (line 66) | arrow::Status
    function append_struct_row_to_dict (line 85) | arrow::Status append_struct_row_to_dict(
    function migrate_v2_to_v3 (line 116) | arrow::Result<MigrationResult> migrate_v2_to_v3(

FILE: c++/pod5_format/migration/v3_to_v4.cpp
  type pod5 (line 11) | namespace pod5 {
    function migrate_v3_to_v4 (line 13) | arrow::Result<MigrationResult> migrate_v3_to_v4(

FILE: c++/pod5_format/read_table_reader.cpp
  type pod5 (line 15) | namespace pod5 {
    function ReadTableReader (line 212) | ReadTableReader & ReadTableReader::operator=(ReadTableReader && other)
    function Status (line 227) | Status ReadTableReader::build_read_id_lookup() const
    function make_read_table_reader (line 331) | Result<ReadTableReader> make_read_table_reader(

FILE: c++/pod5_format/read_table_reader.h
  function namespace (line 17) | namespace arrow {
  type ReadTableRecordColumns (line 37) | struct ReadTableRecordColumns {
  function Dict (line 92) | enum class Dict : std::size_t { Pore, EndReason, RunInfo, Max };
  type IndexData (line 119) | struct IndexData {

FILE: c++/pod5_format/read_table_schema.cpp
  type pod5 (line 6) | namespace pod5 {
    function TableSpecVersion (line 66) | TableSpecVersion ReadTableSchemaDescription::table_version_from_file_v...
    function read_read_table_schema (line 72) | Result<std::shared_ptr<ReadTableSchemaDescription const>> read_read_ta...

FILE: c++/pod5_format/read_table_schema.h
  function namespace (line 13) | namespace arrow {
  function namespace (line 20) | namespace pod5 {

FILE: c++/pod5_format/read_table_utils.cpp
  type pod5 (line 5) | namespace pod5 {

FILE: c++/pod5_format/read_table_utils.h
  function namespace (line 13) | namespace pod5 {
  function ReadEndReason (line 219) | enum class ReadEndReason : std::uint8_t {

FILE: c++/pod5_format/read_table_writer.cpp
  type pod5 (line 12) | namespace pod5 {
    function Status (line 100) | Status ReadTableWriter::close()
    function Status (line 113) | Status ReadTableWriter::write_batch(arrow::RecordBatch const & record_...
    function Status (line 119) | Status ReadTableWriter::write_batch()
    function Status (line 142) | Status ReadTableWriter::reserve_rows()
    function make_read_table_writer (line 152) | Result<ReadTableWriter> make_read_table_writer(

FILE: c++/pod5_format/read_table_writer.h
  function namespace (line 13) | namespace arrow {
  function namespace (line 21) | namespace pod5 {

FILE: c++/pod5_format/read_table_writer_utils.cpp
  type pod5 (line 10) | namespace pod5 {
    type detail (line 12) | namespace detail {
      function get_array_data (line 14) | arrow::Result<std::shared_ptr<arrow::ArrayData>> get_array_data(
    function make_pore_writer (line 41) | arrow::Result<std::shared_ptr<PoreWriter>> make_pore_writer(arrow::Mem...
    function make_end_reason_writer (line 46) | arrow::Result<std::shared_ptr<EndReasonWriter>> make_end_reason_writer...
    function make_run_info_writer (line 61) | arrow::Result<std::shared_ptr<RunInfoWriter>> make_run_info_writer(arr...

FILE: c++/pod5_format/read_table_writer_utils.h
  function namespace (line 19) | namespace pod5 {

FILE: c++/pod5_format/result.h
  function namespace (line 5) | namespace pod5 {

FILE: c++/pod5_format/run_info_table_reader.cpp
  type pod5 (line 14) | namespace pod5 {
    function value_for_map (line 16) | inline std::vector<std::pair<std::string, std::string>> value_for_map(
    function RunInfoTableRecordBatch (line 47) | RunInfoTableRecordBatch & RunInfoTableRecordBatch::operator=(RunInfoTa...
    function RunInfoTableReader (line 107) | RunInfoTableReader & RunInfoTableReader::operator=(RunInfoTableReader ...
    function make_run_info_table_reader (line 248) | Result<RunInfoTableReader> make_run_info_table_reader(

FILE: c++/pod5_format/run_info_table_reader.h
  function namespace (line 17) | namespace arrow {
  function namespace (line 29) | namespace pod5 {

FILE: c++/pod5_format/run_info_table_schema.cpp
  type pod5 (line 6) | namespace pod5 {
    function TableSpecVersion (line 58) | TableSpecVersion RunInfoTableSchemaDescription::table_version_from_fil...
    function read_run_info_table_schema (line 64) | Result<std::shared_ptr<RunInfoTableSchemaDescription const>> read_run_...

FILE: c++/pod5_format/run_info_table_schema.h
  function namespace (line 13) | namespace arrow {
  function namespace (line 20) | namespace pod5 {

FILE: c++/pod5_format/run_info_table_writer.cpp
  type pod5 (line 13) | namespace pod5 {
    function Status (line 82) | Status RunInfoTableWriter::close()
    function Status (line 95) | Status RunInfoTableWriter::write_batch(arrow::RecordBatch const & reco...
    function Status (line 101) | Status RunInfoTableWriter::write_batch()
    function Status (line 124) | Status RunInfoTableWriter::reserve_rows()
    function make_run_info_table_writer (line 134) | Result<RunInfoTableWriter> make_run_info_table_writer(

FILE: c++/pod5_format/run_info_table_writer.h
  function namespace (line 11) | namespace arrow {
  function namespace (line 19) | namespace pod5 {

FILE: c++/pod5_format/schema_field_builder.h
  function namespace (line 10) | namespace pod5 {
  function Status (line 265) | Status append(AppendArgs const &... args)

FILE: c++/pod5_format/schema_metadata.cpp
  type pod5 (line 8) | namespace pod5 {
    function parse_version_number (line 10) | Result<Version> parse_version_number(std::string const & ver)
    function Version (line 57) | Version current_build_version_number()
    function make_schema_key_value_metadata (line 62) | Result<std::shared_ptr<arrow::KeyValueMetadata const>> make_schema_key...
    function read_schema_key_value_metadata (line 84) | Result<SchemaMetadataDescription> read_schema_key_value_metadata(

FILE: c++/pod5_format/schema_metadata.h
  function namespace (line 11) | namespace arrow {
  function namespace (line 15) | namespace pod5 {

FILE: c++/pod5_format/schema_utils.cpp
  type pod5 (line 3) | namespace pod5 {
    function Status (line 21) | Status SchemaDescriptionBase::read_schema(

FILE: c++/pod5_format/schema_utils.h
  function namespace (line 8) | namespace pod5 {

FILE: c++/pod5_format/signal_builder.h
  function namespace (line 14) | namespace pod5 {

FILE: c++/pod5_format/signal_compression.cpp
  type pod5 (line 13) | namespace pod5 {
    class DecompressContext (line 20) | class DecompressContext {
      type DCtxDeleter (line 21) | struct DCtxDeleter {
      method DecompressContext (line 28) | DecompressContext() { m_context.reset(ZSTD_createDCtx()); }
      method ZSTD_DCtx (line 30) | ZSTD_DCtx * get() { return m_context.get(); }
    function compressed_signal_max_size (line 37) | arrow::Result<std::size_t> compressed_signal_max_size(std::size_t samp...
    function compress_signal (line 59) | arrow::Result<std::size_t> compress_signal(
    function compress_signal (line 108) | arrow::Result<std::shared_ptr<arrow::Buffer>> compress_signal(
    function decompress_signal (line 127) | arrow::Status decompress_signal(
    function decompress_signal (line 234) | arrow::Result<std::shared_ptr<arrow::Buffer>> decompress_signal(

FILE: c++/pod5_format/signal_compression.h
  function namespace (line 8) | namespace arrow {
  function namespace (line 13) | namespace pod5 {

FILE: c++/pod5_format/signal_table_reader.cpp
  type pod5 (line 13) | namespace pod5 {
    type SignalTableReaderCacheCleaner (line 15) | struct SignalTableReaderCacheCleaner {
      method make_space_in_table_batches (line 16) | static void make_space_in_table_batches(
    function Status (line 89) | Status SignalTableRecordBatch::extract_signal_row(
    function SignalTableReader (line 192) | SignalTableReader & SignalTableReader::operator=(SignalTableReader && ...
    function Status (line 269) | Status SignalTableReader::extract_samples(
    function SignalType (line 317) | SignalType SignalTableReader::signal_type() const { return m_field_loc...
    function make_signal_table_reader (line 320) | Result<SignalTableReader> make_signal_table_reader(

FILE: c++/pod5_format/signal_table_reader.h
  function namespace (line 17) | namespace arrow {
  function namespace (line 29) | namespace pod5 {

FILE: c++/pod5_format/signal_table_schema.cpp
  type pod5 (line 8) | namespace pod5 {
    function make_signal_table_schema (line 10) | std::shared_ptr<arrow::Schema> make_signal_table_schema(
    function read_signal_table_schema (line 41) | Result<SignalTableSchemaDescription> read_signal_table_schema(

FILE: c++/pod5_format/signal_table_schema.h
  function namespace (line 9) | namespace arrow {
  function namespace (line 14) | namespace pod5 {

FILE: c++/pod5_format/signal_table_utils.h
  function namespace (line 3) | namespace pod5 {

FILE: c++/pod5_format/signal_table_writer.cpp
  type pod5 (line 16) | namespace pod5 {
    function Status (line 132) | Status SignalTableWriter::close()
    function SignalType (line 146) | SignalType SignalTableWriter::signal_type() const { return m_field_loc...
    function Status (line 148) | Status SignalTableWriter::write_batch(arrow::RecordBatch const & recor...
    function Status (line 154) | Status SignalTableWriter::write_batch()
    function Status (line 182) | Status SignalTableWriter::reserve_rows()
    function make_signal_table_writer (line 198) | Result<SignalTableWriter> make_signal_table_writer(

FILE: c++/pod5_format/signal_table_writer.h
  function namespace (line 12) | namespace arrow {
  function namespace (line 20) | namespace pod5 {

FILE: c++/pod5_format/svb16/common.hpp
  function svb16_popcount (line 30) | inline int svb16_popcount(unsigned int i)

FILE: c++/pod5_format/svb16/decode.hpp
  type svb16 (line 14) | namespace svb16 {
    function decode_input_buffer_padding_byte_count (line 19) | inline std::size_t decode_input_buffer_padding_byte_count()
    function decode (line 29) | size_t decode(gsl::span<Int16T> out, gsl::span<uint8_t const> in, Int1...
    function validate (line 42) | inline bool validate(gsl::span<uint8_t const> compressed_input, std::s...

FILE: c++/pod5_format/svb16/decode_scalar.hpp
  type svb16 (line 12) | namespace svb16 {
    type detail (line 13) | namespace detail {
      function zigzag_decode (line 14) | inline uint16_t zigzag_decode(uint16_t val)
      function decode_data (line 19) | inline uint16_t decode_data(gsl::span<uint8_t const>::iterator & dat...
    function SVB16_IF_CONSTEXPR (line 62) | SVB16_IF_CONSTEXPR(UseZigzag) { value = detail::zigzag_decode(value); }
    function SVB16_IF_CONSTEXPR (line 63) | SVB16_IF_CONSTEXPR(UseDelta)

FILE: c++/pod5_format/svb16/decode_x64.hpp
  type svb16 (line 16) | namespace svb16 {
    type detail (line 17) | namespace detail {
      function __m128i (line 18) | [[gnu::target("ssse3")]] inline __m128i zigzag_decode(__m128i val)
      function __m128i (line 29) | [[gnu::target("ssse3")]] inline __m128i unpack(uint32_t key, uint8_t...
      function store_8 (line 42) | [[gnu::target("ssse3")]] inline void store_8(Int16T * to, __m128i va...
    function SVB16_IF_CONSTEXPR (line 97) | SVB16_IF_CONSTEXPR(UseDelta) { prev_reg = _mm_set1_epi16(prev); }

FILE: c++/pod5_format/svb16/encode.hpp
  type svb16 (line 11) | namespace svb16 {
    function encode (line 14) | size_t encode(Int16T const * in, uint8_t * SVB_RESTRICT out, uint32_t ...

FILE: c++/pod5_format/svb16/encode_scalar.hpp
  type svb16 (line 9) | namespace svb16 {
    type detail (line 10) | namespace detail {
      function zigzag_encode (line 11) | inline uint16_t zigzag_encode(uint16_t val)
    function SVB16_IF_CONSTEXPR (line 38) | SVB16_IF_CONSTEXPR(UseDelta)
    function else (line 45) | else SVB16_IF_CONSTEXPR(UseZigzag) {

FILE: c++/pod5_format/svb16/encode_x64.hpp
  type svb16 (line 14) | namespace svb16 {
    type detail (line 15) | namespace detail {
      function __m128i (line 16) | [[gnu::target("ssse3")]] inline __m128i delta(__m128i curr, __m128i ...
      function __m128i (line 21) | [[gnu::target("ssse3")]] inline __m128i zigzag_encode(__m128i val)
      function __m128i (line 27) | [[gnu::target("ssse3")]] inline __m128i load_8(Int16T const * from, ...
    function SVB16_IF_CONSTEXPR (line 61) | SVB16_IF_CONSTEXPR(UseDelta) { prev_reg = _mm_set1_epi16(prev); }
    function SVB16_IF_CONSTEXPR (line 111) | SVB16_IF_CONSTEXPR(UseDelta) { prev = _mm_extract_epi16(prev_reg, 7); }

FILE: c++/pod5_format/svb16/generate_shuffle_tables.py
  function encode_table_row (line 1) | def encode_table_row(control):
  function decode_table_row (line 17) | def decode_table_row(control):
  function print_x64_encode_table (line 31) | def print_x64_encode_table():
  function print_x64_decode_table (line 39) | def print_x64_decode_table():

FILE: c++/pod5_format/svb16/intrinsics.hpp
  type svb16 (line 15) | namespace svb16 { namespace detail {
    type detail (line 15) | namespace detail {
      function __m128i (line 16) | [[gnu::target("sse2")]] inline constexpr __m128i m128i_from_bytes(

FILE: c++/pod5_format/svb16/simd_detect_x64.hpp
  function has_ssse3 (line 14) | inline constexpr bool has_ssse3() { return true; }
  function has_sse4_1 (line 16) | inline constexpr bool has_sse4_1() { return true; }
  type CpuidResult (line 20) | struct CpuidResult {
  function CpuidResult (line 27) | inline CpuidResult cpuid(unsigned int leaf, unsigned int subleaf)
  function cpuid_leaf1_ecx (line 47) | inline unsigned int cpuid_leaf1_ecx()
  function has_ssse3 (line 55) | inline constexpr bool has_ssse3() { return true; }
  function has_ssse3 (line 57) | inline bool has_ssse3() { return (cpuid_leaf1_ecx() & (1 << 9)) != 0; }
  function has_sse4_1 (line 60) | inline bool has_sse4_1() { return (cpuid_leaf1_ecx() & (1 << 19)) != 0; }

FILE: c++/pod5_format/svb16/streamvbytedelta_decode_16.c
  function zigzag_decode_16 (line 6) | static inline uint16_t zigzag_decode_16(uint16_t val)
  function _decode_data (line 11) | static inline uint16_t _decode_data(uint8_t const ** dataPtrPtr, uint8_t...
  function streamvbyte_zigzag_delta_decode_16 (line 63) | size_t streamvbyte_zigzag_delta_decode_16(

FILE: c++/pod5_format/svb16/streamvbytedelta_encode_16.c
  function _zigzag_encode_16 (line 11) | static inline uint16_t _zigzag_encode_16(uint16_t val)
  function _encode_data (line 16) | static uint8_t _encode_data(uint16_t val, uint8_t * __restrict__ * dataP...
  function streamvbyte_zigzag_delta_encode_16 (line 65) | size_t streamvbyte_zigzag_delta_encode_16(

FILE: c++/pod5_format/svb16/streamvbytedelta_x64_decode_16.c
  function STREAMVBYTE_TARGET_SSSE3 (line 7) | STREAMVBYTE_TARGET_SSSE3
  function __m128i (line 22) | static inline __m128i _decode_avx(uint32_t key, uint8_t const * __restri...
  function _write_avx (line 37) | static inline void _write_avx(uint16_t * out, __m128i Vec)
  function __m128i (line 45) | static inline __m128i _write_16bit_avx_d1(uint16_t * out, __m128i Vec, _...

FILE: c++/pod5_format/svb16/streamvbytedelta_x64_encode_16.c
  function STREAMVBYTE_TARGET_SSSE3 (line 10) | STREAMVBYTE_TARGET_SSSE3
  function __m128i (line 20) | static __m128i zigzag_16(__m128i buf)
  function streamvbyte_zigzag_delta_encode_SSSE3_d1_init (line 29) | size_t streamvbyte_zigzag_delta_encode_SSSE3_d1_init(

FILE: c++/pod5_format/svb16/svb16.h
  function svb16_key_length (line 11) | inline uint32_t svb16_key_length(uint32_t count)
  function svb16_max_encoded_length (line 18) | inline uint32_t svb16_max_encoded_length(uint32_t count)

FILE: c++/pod5_format/table_reader.cpp
  type pod5 (line 7) | namespace pod5 {
    function ReadRecordBatchAndValidate (line 53) | Result<std::shared_ptr<arrow::RecordBatch>> ReadRecordBatchAndValidate(

FILE: c++/pod5_format/table_reader.h
  function namespace (line 8) | namespace arrow {
  function namespace (line 17) | namespace pod5 {

FILE: c++/pod5_format/thread_pool.cpp
  type pod5 (line 13) | namespace pod5 {
    class ThreadPoolImpl (line 17) | class ThreadPoolImpl : public ThreadPool, public std::enable_shared_fr...
      method ThreadPoolImpl (line 19) | ThreadPoolImpl(std::size_t worker_count)
      method run_thread (line 29) | void run_thread()
      method post (line 80) | void post(std::function<void()> callback) override
      method post (line 93) | void post(std::function<void()> callback, uint64_t const strand_id)
      method stop_and_drain (line 113) | void stop_and_drain() override
      method wait_for_drain (line 129) | void wait_for_drain() override
      type WorkItem (line 144) | struct WorkItem {
    class StrandImpl (line 163) | class StrandImpl : public ThreadPoolStrand {
      method StrandImpl (line 165) | StrandImpl(std::shared_ptr<ThreadPoolImpl> pool, uint64_t const stra...
      method post (line 171) | void post(std::function<void()> callback) override
    function make_thread_pool (line 194) | std::shared_ptr<ThreadPool> make_thread_pool(std::size_t worker_threads)

FILE: c++/pod5_format/thread_pool.h
  function namespace (line 8) | namespace pod5 {

FILE: c++/pod5_format/tuple_utils.h
  function namespace (line 6) | namespace pod5 { namespace detail {

FILE: c++/pod5_format/types.cpp
  type pod5 (line 9) | namespace pod5 {
    function Uuid (line 11) | Uuid const * UuidArray::raw_values() const
    function Uuid (line 17) | Uuid UuidArray::Value(int64_t i) const
    function make_read_id_builder (line 103) | std::unique_ptr<arrow::FixedSizeBinaryBuilder> make_read_id_builder(ar...
    function register_extension_types (line 138) | pod5::Status register_extension_types()
    function unregister_extension_types (line 148) | pod5::Status unregister_extension_types()
    function check_extension_types_registered (line 163) | bool check_extension_types_registered()

FILE: c++/pod5_format/types.h
  function namespace (line 11) | namespace pod5 {

FILE: c++/pod5_format/uuid.h
  function namespace (line 36) | namespace pod5 {
  function swap (line 137) | void swap(Uuid & other) noexcept { m_data.swap(other.m_data); }
  function to_c_array (line 143) | void to_c_array(value_type (&arr)[16]) const noexcept
  function std (line 164) | [[nodiscard]] constexpr static std::optional<Uuid> from_string(
  function swap (line 258) | inline void swap(Uuid & lhs, Uuid & rhs) noexcept { lhs.swap(rhs); }
  function explicit (line 265) | explicit BasicUuidRandomGenerator(engine_type & gen) : generator(&gen) {}
  function explicit (line 267) | explicit BasicUuidRandomGenerator(engine_type * gen) : generator(gen) {}
  function Uuid (line 269) | [[nodiscard]] Uuid operator()()
  function namespace (line 296) | namespace std {

FILE: c++/pod5_format_pybind/api.h
  function std (line 22) | inline std::shared_ptr<pod5::FileWriter> create_file(
  function pod5 (line 35) | inline pod5::RecoveryDetails recover_file(
  function class (line 47) | class Pod5SignalCacheBatch {
  function get_file_read_table_location (line 179) | struct Pod5FileReaderPtr {
  function close (line 204) | void close() { reader = nullptr; }
  function Pod5FileReaderPtr (line 261) | inline Pod5FileReaderPtr open_file(char const * filename)
  function write_updated_file_to_dest (line 267) | inline void write_updated_file_to_dest(Pod5FileReaderPtr source, char co...
  function pod5 (line 273) | inline pod5::RunInfoDictionaryIndex FileWriter_add_run_info(
  function FileWriter_add_reads_pre_compressed (line 435) | inline void FileWriter_add_reads_pre_compressed(
  function decompress_signal_wrapper (line 526) | inline void decompress_signal_wrapper(
  function compress_signal_wrapper (line 537) | inline std::size_t compress_signal_wrapper(
  function vbz_compressed_signal_max_size (line 550) | inline std::size_t vbz_compressed_signal_max_size(std::size_t sample_count)
  function load_read_id_iterable (line 557) | inline std::size_t load_read_id_iterable(

FILE: c++/pod5_format_pybind/bindings.cpp
  function PYBIND11_MODULE (line 7) | PYBIND11_MODULE(pod5_format_pybind, m)

FILE: c++/pod5_format_pybind/repack/repack_functions.h
  function namespace (line 17) | namespace repack {
  type RequestedSignalReads (line 186) | struct RequestedSignalReads {
  type ReadSignal (line 257) | struct ReadSignal {

FILE: c++/pod5_format_pybind/repack/repack_output.cpp
  type repack (line 10) | namespace repack {
    type is_not_nullptr (line 13) | struct is_not_nullptr {
    type get_name (line 22) | struct get_name{
    function dump_queued_items (line 30) | void dump_queued_items(T const& queued) {
    type Pod5RepackerOutputThreadState (line 46) | struct Pod5RepackerOutputThreadState {
      method Pod5RepackerOutputThreadState (line 47) | Pod5RepackerOutputThreadState(std::shared_ptr<ReadsTableDictionaryMa...
    type Pod5RepackerOutputState (line 55) | struct Pod5RepackerOutputState {
      method Pod5RepackerOutputState (line 56) | Pod5RepackerOutputState(
      method Pod5RepackerOutputThreadState (line 68) | Pod5RepackerOutputThreadState * get_thread_state()
    type StateProgressResult (line 97) | struct StateProgressResult {
      method StateProgressResult (line 98) | StateProgressResult() = default;
      method StateProgressResult (line 100) | StateProgressResult(std::vector<states::shared_variant> && _new_states)
    type StateOperator (line 108) | struct StateOperator {
      method StateOperator (line 109) | StateOperator(Pod5RepackerOutputState * _progress_state) : progress_...
      method ARROW_ASSIGN_OR_RAISE (line 137) | ARROW_ASSIGN_OR_RAISE(

FILE: c++/pod5_format_pybind/repack/repack_output.h
  type Pod5RepackerOutputState (line 17) | struct Pod5RepackerOutputState
  function set_error (line 61) | void set_error(arrow::Status error)

FILE: c++/pod5_format_pybind/repack/repack_states.h
  function namespace (line 14) | namespace repack { namespace states {

FILE: c++/pod5_format_pybind/repack/repack_utils.h
  function namespace (line 10) | namespace repack {
  function class (line 27) | class ReadsTableDictionaryManager {
  function class (line 94) | class ReadsTableDictionaryThreadCache {

FILE: c++/pod5_format_pybind/repack/repacker.cpp
  type repack (line 7) | namespace repack {
    function repacker_add_reads_preconditions (line 11) | void repacker_add_reads_preconditions(

FILE: c++/pod5_format_pybind/repack/repacker.h
  function namespace (line 11) | namespace repack {

FILE: c++/pod5_format_pybind/subset.cpp
  type io_limits (line 28) | namespace io_limits {
    function clamp_open_inputs (line 37) | std::size_t clamp_open_inputs(std::size_t soft_limit, std::size_t outp...
    function clamp_open_outputs (line 47) | std::size_t clamp_open_outputs(std::size_t soft_limit)
    function detect_soft_limit (line 62) | std::size_t detect_soft_limit()
  class ProgressBar (line 84) | class ProgressBar {
    method ProgressBar (line 88) | ProgressBar() {}
    method set_task (line 92) | void set_task(std::string const & task_name)
    method update_max_steps (line 98) | void update_max_steps(std::size_t max_steps) { this->m_max_steps = max...
    method update (line 100) | void update(std::size_t current_step)
    method print_progress (line 109) | void print_progress()
  function subset_pod5s_with_mapping (line 136) | void subset_pod5s_with_mapping(

FILE: c++/pod5_format_pybind/utils.h
  function raise_error (line 5) | inline void raise_error(arrow::Status const & status)
  function throw_on_error (line 35) | inline void throw_on_error(pod5::Status const & s)

FILE: c++/test/TemporaryDirectory.h
  function namespace (line 7) | namespace ont { namespace testutils {

FILE: c++/test/c_api_null_input.cpp
  function pod5_reset_error (line 11) | void pod5_reset_error()
  type detail (line 18) | namespace detail {
    function ptr_idx_to_arg_idx (line 21) | constexpr std::size_t ptr_idx_to_arg_idx()
    function make_ptr_null_impl (line 38) | void make_ptr_null_impl(std::tuple<Args...> & args, std::uint64_t vali...
    function make_ptrs_null (line 54) | void make_ptrs_null(
    function unpack_and_call (line 63) | auto unpack_and_call(
  function call_with_nulls (line 74) | void call_with_nulls(pod5_error_t (*func)(Args...), Args... args)

FILE: c++/test/c_api_test_utils.h
  function namespace (line 33) | namespace testutils {
  function class (line 45) | class IsPod5COk : public Catch::MatcherBase<Pod5C_Result> {
  function Pod5C_Result (line 57) | struct Catch::StringMaker<testutils::Pod5C_Result> {

FILE: c++/test/c_api_tests.cpp
  type Pod5ReadId (line 17) | struct Pod5ReadId {
    method Pod5ReadId (line 18) | Pod5ReadId() = default;
    method Pod5ReadId (line 20) | Pod5ReadId(pod5::Uuid const & uid) { uid.to_c_array(read_id); }
    method as_uuid (line 22) | pod5::Uuid as_uuid() const { return pod5::Uuid{read_id}; }

FILE: c++/test/file_reader_writer_tests.cpp
  function run_file_reader_writer_tests (line 26) | void run_file_reader_writer_tests(
  type ReadData (line 239) | struct ReadData {
  function touch (line 406) | static void touch(std::filesystem::path const & path) { std::ofstream co...
  function write_zeros (line 409) | static void write_zeros(std::filesystem::path const & path)
  function file_writing_started (line 418) | static bool file_writing_started(std::filesystem::path const & file_path)
  function files_ready_to_recover (line 443) | static bool files_ready_to_recover(std::filesystem::path const & directo...
  function wait_for_files_to_recover (line 453) | static void wait_for_files_to_recover(std::filesystem::path const & dire...
  function create_files_for_recovery (line 468) | static std::filesystem::path create_files_for_recovery(
  function ends_with (line 558) | static bool ends_with(std::string const & search_in, std::string const &...
  function escape_for_regex (line 575) | static std::string escape_for_regex(std::string const & input)

FILE: c++/test/output_stream_tests.cpp
  function get_test_data (line 14) | std::shared_ptr<arrow::Buffer> get_test_data()
  function read_file (line 27) | std::vector<char> read_file(char const * filename)
  function check_file_contents (line 34) | void check_file_contents(char const * filename)
  function run_output_stream_test (line 48) | void run_output_stream_test(std::shared_ptr<arrow::io::OutputStream> out...

FILE: c++/test/svb16_scalar_tests.cpp
  function test_scalar_encode_scalar_decode (line 15) | void test_scalar_encode_scalar_decode()

FILE: c++/test/svb16_x64_tests.cpp
  function test_sse_encode_scalar_decode (line 18) | void test_sse_encode_scalar_decode()

FILE: c++/test/test_utils.h
  function match (line 17) | bool match(arrow::Status const & status) const override { return status....
  function match (line 27) | bool match(arrow::Result<T> const & status) const override { return stat...

FILE: c++/test/utils.h
  function arrow (line 39) | inline arrow::Status remove_file_if_exists(std::string const & file)

FILE: conanfile.py
  class Pod5Conan (line 9) | class Pod5Conan(ConanFile):
    method _setup_third_party_deps_packaging (line 36) | def _setup_third_party_deps_packaging(self):
    method _licenses_path (line 56) | def _licenses_path(self):
    method _copy_licenses (line 60) | def _copy_licenses(self):
    method layout (line 73) | def layout(self):
    method requirements (line 76) | def requirements(self):
    method build_requirements (line 97) | def build_requirements(self):
    method generate (line 105) | def generate(self):
    method build (line 127) | def build(self):
    method package (line 132) | def package(self):
    method package_info (line 150) | def package_info(self):

FILE: fuzz/fuzz_compress.cpp
  function setenv (line 14) | static int setenv(char const * name, char const * value, int) { return _...
  function CheckPod5 (line 27) | void CheckPod5(pod5_error_t err, char const * msg)
  function LLVMFuzzerInitialize (line 42) | int LLVMFuzzerInitialize(int * argc, char *** argv)
  function LLVMFuzzerTestOneInput (line 55) | int LLVMFuzzerTestOneInput(uint8_t const * data, size_t size)

FILE: fuzz/fuzz_file.cpp
  function setenv (line 19) | static int setenv(char const * name, char const * value, int) { return _...
  function check_pod5_ok (line 46) | void check_pod5_ok(pod5_error_t err, char const * msg)
  function check_pod5_consistency (line 55) | void check_pod5_consistency(pod5_error_t err, char const * msg)
  function keep_result (line 74) | void keep_result(T && t)
  function validate_string (line 81) | void validate_string(char const * ptr)
  type POD5FileCloser (line 88) | struct POD5FileCloser {
  function LLVMFuzzerInitialize (line 100) | int LLVMFuzzerInitialize(int * argc, char *** argv)
  function LLVMFuzzerTestOneInput (line 116) | int LLVMFuzzerTestOneInput(uint8_t const * data, size_t size)

FILE: fuzz/runner.cpp
  function run_one (line 19) | void run_one(bool verbose, std::filesystem::path const & path)
  function run_recursive (line 35) | void run_recursive(bool verbose, std::filesystem::path const & path)
  function main (line 48) | int main(int argc, char ** argv)

FILE: pod5_make_version.py
  function create_pod5_version_cmake (line 10) | def create_pod5_version_cmake():
  function copy_version_py (line 26) | def copy_version_py():

FILE: python/lib_pod5/setup.py
  class BinaryInstall (line 32) | class BinaryInstall(install):
    method __init__ (line 33) | def __init__(self, dist):
  class BdistWheel (line 42) | class BdistWheel(bdist_wheel):
    method finalize_options (line 43) | def finalize_options(self):
    method get_tag (line 47) | def get_tag(self):

FILE: python/lib_pod5/src/lib_pod5/pod5_format_pybind.pyi
  class CleanupError (line 16) | class CleanupError:
    method __init__ (line 19) | def __init__(self) -> None: ...
  class EmbeddedFileData (line 21) | class EmbeddedFileData:
    method __init__ (line 22) | def __init__(self, *args, **kwargs) -> None: ...
    method length (line 24) | def length(self) -> int: ...
    method offset (line 26) | def offset(self) -> int: ...
    method file_path (line 28) | def file_path(self) -> str: ...
  class FileWriter (line 30) | class FileWriter:
    method __init__ (line 31) | def __init__(self, *args, **kwargs) -> None: ...
    method add_end_reason (line 32) | def add_end_reason(self, end_reason_enum: int) -> int: ...
    method add_pore (line 33) | def add_pore(self, pore_type: str) -> int: ...
    method add_reads (line 34) | def add_reads(
    method add_reads_pre_compressed (line 59) | def add_reads_pre_compressed(
    method add_run_info (line 86) | def add_run_info(
    method close (line 109) | def close(self) -> None: ...
  class FileWriterOptions (line 111) | class FileWriterOptions:
    method __init__ (line 116) | def __init__(self, *args, **kwargs) -> None: ...
  class Pod5AsyncSignalLoader (line 118) | class Pod5AsyncSignalLoader:
    method __init__ (line 119) | def __init__(self, *args, **kwargs) -> None: ...
    method release_next_batch (line 120) | def release_next_batch(self) -> Pod5SignalCacheBatch: ...
  class Pod5FileReader (line 122) | class Pod5FileReader:
    method __init__ (line 123) | def __init__(self, *args, **kwargs) -> None: ...
    method batch_get_signal (line 124) | def batch_get_signal(
    method batch_get_signal_batches (line 127) | def batch_get_signal_batches(
    method batch_get_signal_selection (line 133) | def batch_get_signal_selection(
    method close (line 140) | def close(self) -> None: ...
    method get_file_read_table_location (line 141) | def get_file_read_table_location(self) -> EmbeddedFileData: ...
    method get_file_run_info_table_location (line 142) | def get_file_run_info_table_location(self) -> EmbeddedFileData: ...
    method get_file_signal_table_location (line 143) | def get_file_signal_table_location(self) -> EmbeddedFileData: ...
    method get_file_version_pre_migration (line 144) | def get_file_version_pre_migration(self) -> str: ...
    method plan_traversal (line 145) | def plan_traversal(
  class Pod5RepackerOutput (line 152) | class Pod5RepackerOutput:
    method __init__ (line 153) | def __init__(self, *args, **kwargs) -> None: ...
  class Pod5SignalCacheBatch (line 155) | class Pod5SignalCacheBatch:
    method __init__ (line 156) | def __init__(self, *args, **kwargs) -> None: ...
    method batch_index (line 158) | def batch_index(self) -> int: ...
    method sample_count (line 160) | def sample_count(self) -> npt.NDArray[np.uint64]: ...
    method samples (line 162) | def samples(self) -> List[npt.NDArray[np.int16]]: ...
  class RecoverFileOptions (line 164) | class RecoverFileOptions:
    method __init__ (line 167) | def __init__(self) -> None: ...
  class RecoveredRowCounts (line 169) | class RecoveredRowCounts:
    method __init__ (line 173) | def __init__(self) -> None: ...
  class RecoveryDetails (line 175) | class RecoveryDetails:
    method __init__ (line 178) | def __init__(self) -> None: ...
  class Repacker (line 180) | class Repacker:
    method __init__ (line 181) | def __init__(self) -> None: ...
    method add_all_reads_to_output (line 182) | def add_all_reads_to_output(
    method add_output (line 185) | def add_output(
    method add_selected_reads_to_output (line 188) | def add_selected_reads_to_output(
    method finish (line 195) | def finish(self) -> None: ...
    method is_complete (line 197) | def is_complete(self) -> bool: ...
    method open_file_readers (line 199) | def open_file_readers(self) -> int: ...
    method reads_completed (line 201) | def reads_completed(self) -> int: ...
  function compress_signal (line 203) | def compress_signal(
  function create_file (line 206) | def create_file(
  function recover_file (line 209) | def recover_file(
  function decompress_signal (line 212) | def decompress_signal(
  function format_read_id_to_str (line 216) | def format_read_id_to_str(
  function get_error_string (line 219) | def get_error_string() -> str: ...
  function load_read_id_iterable (line 220) | def load_read_id_iterable(
  function open_file (line 223) | def open_file(filename: str) -> Pod5FileReader: ...
  function update_file (line 224) | def update_file(reader: Pod5FileReader, output: str): ...
  function vbz_compressed_signal_max_size (line 225) | def vbz_compressed_signal_max_size(sample_count: int) -> int: ...

FILE: python/lib_pod5/src/test/test_lib_pod5.py
  function test_create_file (line 10) | def test_create_file(tmp_path: Path) -> None:
  function test_open_file (line 21) | def test_open_file(tmp_path: Path) -> None:

FILE: python/pod5/examples/find_all_reads.py
  function main (line 9) | def main():

FILE: python/pod5/examples/find_specific_reads.py
  function main (line 12) | def main():

FILE: python/pod5/src/pod5/api_utils.py
  class Pod5ApiException (line 14) | class Pod5ApiException(Exception):
  function pack_read_ids (line 18) | def pack_read_ids(
  function format_read_ids (line 43) | def format_read_ids(
  function deprecation_warning (line 64) | def deprecation_warning(deprecated: str, alternate: str) -> None:
  function safe_close (line 83) | def safe_close(obj: Any, attr: str) -> None:

FILE: python/pod5/src/pod5/dataset.py
  class DatasetReader (line 27) | class DatasetReader:
    method __init__ (line 28) | def __init__(
    method __iter__ (line 91) | def __iter__(self) -> Generator[ReadRecord, None, None]:
    method __len__ (line 94) | def __len__(self) -> int:
    method num_reads (line 99) | def num_reads(self) -> int:
    method paths (line 119) | def paths(self) -> List[Path]:
    method read_ids (line 124) | def read_ids(self) -> Generator[str, None, None]:
    method reads (line 135) | def reads(
    method get_read (line 170) | def get_read(self, read_id: str) -> Optional[ReadRecord]:
    method _init_get_reader (line 204) | def _init_get_reader(maxsize: Optional[int]) -> Callable[[Path], Reader]:
    method get_reader (line 216) | def get_reader(self, path: PathOrStr) -> Reader:
    method get_path (line 231) | def get_path(self, read_id: str) -> Optional[Path]:
    method clear_readers (line 264) | def clear_readers(self) -> None:
    method clear_index (line 268) | def clear_index(self) -> None:
    method has_duplicate (line 272) | def has_duplicate(self) -> bool:
    method _collect_dataset (line 285) | def _collect_dataset(
    method index_read_ids (line 307) | def index_read_ids(self) -> None:
    method _index_read_ids (line 315) | def _index_read_ids(self) -> None:
    method _issue_duplicate_read_warning (line 327) | def _issue_duplicate_read_warning(self) -> None:
    method _run_max_workers (line 332) | def _run_max_workers(
    method __enter__ (line 348) | def __enter__(self) -> "DatasetReader":
    method __exit__ (line 351) | def __exit__(self, *exc_details) -> None:

FILE: python/pod5/src/pod5/pod5_types.py
  class EndReasonEnum (line 21) | class EndReasonEnum(enum.Enum):
  class EndReason (line 53) | class EndReason:
    method name (line 72) | def name(self) -> str:
    method from_reason_with_default_forced (line 77) | def from_reason_with_default_forced(cls, reason: EndReasonEnum) -> "En...
  class Calibration (line 86) | class Calibration:
    method from_range (line 105) | def from_range(
  class Pore (line 113) | class Pore:
  class RunInfo (line 137) | class RunInfo:
  class ShiftScalePair (line 242) | class ShiftScalePair:
    method __eq__ (line 248) | def __eq__(self, other: object) -> bool:
  class BaseRead (line 259) | class BaseRead:
  class Read (line 329) | class Read(BaseRead):
    method sample_count (line 363) | def sample_count(self) -> int:
  class CompressedRead (line 369) | class CompressedRead(BaseRead):
    method sample_count (line 406) | def sample_count(self) -> int:
    method decompressed_signal (line 411) | def decompressed_signal(self) -> npt.NDArray[np.int16]:

FILE: python/pod5/src/pod5/reader.py
  class ReadRecord (line 121) | class ReadRecord:
    method __init__ (line 126) | def __init__(
    method read_id (line 142) | def read_id(self) -> UUID:
    method read_number (line 149) | def read_number(self) -> int:
    method start_sample (line 156) | def start_sample(self) -> int:
    method num_samples (line 163) | def num_samples(self) -> int:
    method median_before (line 170) | def median_before(self) -> float:
    method num_minknow_events (line 177) | def num_minknow_events(self) -> int:
    method tracked_scaling (line 187) | def tracked_scaling(self) -> ShiftScalePair:
    method predicted_scaling (line 200) | def predicted_scaling(self) -> ShiftScalePair:
    method num_reads_since_mux_change (line 213) | def num_reads_since_mux_change(self) -> int:
    method time_since_mux_change (line 223) | def time_since_mux_change(self) -> float:
    method open_pore_level (line 230) | def open_pore_level(self) -> float:
    method pore (line 239) | def pore(self) -> Pore:
    method calibration (line 250) | def calibration(self) -> Calibration:
    method calibration_digitisation (line 260) | def calibration_digitisation(self) -> int:
    method calibration_range (line 269) | def calibration_range(self) -> float:
    method end_reason (line 278) | def end_reason(self) -> EndReason:
    method run_info (line 290) | def run_info(self) -> RunInfo:
    method end_reason_index (line 297) | def end_reason_index(self) -> int:
    method run_info_index (line 305) | def run_info_index(self) -> int:
    method sample_count (line 312) | def sample_count(self) -> int:
    method byte_count (line 319) | def byte_count(self) -> int:
    method has_cached_signal (line 326) | def has_cached_signal(self) -> bool:
    method signal (line 333) | def signal(self) -> npt.NDArray[np.int16]:
    method signal_pa (line 372) | def signal_pa(self) -> npt.NDArray[np.float32]:
    method signal_for_chunk (line 383) | def signal_for_chunk(self, index: int) -> npt.NDArray[np.int16]:
    method signal_rows (line 397) | def signal_rows(self) -> List[SignalRowInfo]:
    method calibrate_signal_array (line 425) | def calibrate_signal_array(
    method _find_signal_row_index (line 439) | def _find_signal_row_index(self, signal_row: int) -> Tuple[Signal, int...
    method _get_signal_for_row (line 454) | def _get_signal_for_row(self, signal_row: int) -> npt.NDArray[np.int16]:
    method to_read (line 475) | def to_read(self) -> Read:
  class ReadRecordBatch (line 502) | class ReadRecordBatch:
    method __init__ (line 507) | def __init__(self, reader: "Reader", batch: pa.RecordBatch):
    method columns (line 518) | def columns(self) -> ReadRecordV4Columns:
    method set_cached_signal (line 529) | def set_cached_signal(self, signal_cache: p5b.Pod5SignalCacheBatch) ->...
    method set_selected_batch_rows (line 533) | def set_selected_batch_rows(self, selected_batch_rows: Iterable[int]) ...
    method reads (line 537) | def reads(self) -> Generator[ReadRecord, None, None]:
    method get_read (line 564) | def get_read(self, row: int) -> ReadRecord:
    method num_reads (line 569) | def num_reads(self) -> int:
    method read_id_column (line 574) | def read_id_column(self) -> pa.FixedSizeBinaryArray:
    method read_number_column (line 583) | def read_number_column(self) -> pa.UInt32Array:
    method cached_sample_count_column (line 592) | def cached_sample_count_column(self) -> npt.NDArray[np.uint64]:
    method cached_samples_column (line 601) | def cached_samples_column(self) -> List[npt.NDArray[np.int16]]:
  class ArrowTableHandle (line 610) | class ArrowTableHandle:
    method __init__ (line 613) | def __init__(
    method _open_without_mmap (line 660) | def _open_without_mmap(self) -> pa.PythonFile:
    method _open_with_mmap (line 688) | def _open_with_mmap(self) -> pa.BufferReader:
    method reader (line 715) | def reader(self) -> pa.ipc.RecordBatchFileReader:
    method stream (line 723) | def stream(self) -> Union[pa.PythonFile, pa.NativeFile]:
    method close (line 730) | def close(self) -> None:
    method __enter__ (line 746) | def __enter__(self) -> "ArrowTableHandle":
    method __exit__ (line 749) | def __exit__(self, *exc_details) -> None:
    method __del__ (line 752) | def __del__(self):
  class Reader (line 756) | class Reader:
    method __init__ (line 761) | def __init__(self, path: PathOrStr):
    method _open_arrow_table_handles (line 804) | def _open_arrow_table_handles(
    method __enter__ (line 826) | def __enter__(self) -> "Reader":
    method __exit__ (line 829) | def __exit__(self, *exc_details) -> None:
    method __iter__ (line 832) | def __iter__(self) -> Generator[ReadRecord, None, None]:
    method close (line 836) | def close(self) -> None:
    method path (line 855) | def path(self) -> Path:
    method inner_file_reader (line 860) | def inner_file_reader(self) -> p5b.Pod5FileReader:
    method read_table (line 867) | def read_table(self) -> pa.ipc.RecordBatchFileReader:
    method run_info_table (line 874) | def run_info_table(self) -> pa.ipc.RecordBatchFileReader:
    method signal_table (line 881) | def signal_table(self) -> pa.ipc.RecordBatchFileReader:
    method file_version (line 888) | def file_version(self) -> packaging.version.Version:
    method file_version_pre_migration (line 893) | def file_version_pre_migration(self) -> packaging.version.Version:
    method writing_software (line 898) | def writing_software(self) -> str:
    method file_identifier (line 902) | def file_identifier(self) -> UUID:
    method reads_table_version (line 906) | def reads_table_version(self) -> int:
    method is_vbz_compressed (line 910) | def is_vbz_compressed(self) -> bool:
    method signal_batch_row_count (line 919) | def signal_batch_row_count(self) -> int:
    method batch_count (line 929) | def batch_count(self) -> int:
    method num_reads (line 936) | def num_reads(self) -> int:
    method read_ids_raw (line 948) | def read_ids_raw(self) -> pa.ChunkedArray:
    method read_ids (line 958) | def read_ids(self) -> List[str]:
    method get_batch (line 978) | def get_batch(self, index: int) -> ReadRecordBatch:
    method read_batches (line 989) | def read_batches(
    method reads (line 1027) | def reads(
    method _reads (line 1057) | def _reads(
    method _select_reads (line 1065) | def _select_reads(
    method _reads_batches (line 1076) | def _reads_batches(
    method _read_some_batches (line 1093) | def _read_some_batches(
    method _select_read_batches (line 1113) | def _select_read_batches(
    method _plan_traversal (line 1151) | def _plan_traversal(
    method _get_signal_batch (line 1192) | def _get_signal_batch(self, batch_id: int) -> Signal:
    method _lookup_run_info (line 1204) | def _lookup_run_info(self, batch: ReadRecordBatch, batch_row_id: int) ...
    method __del__ (line 1237) | def __del__(self):

FILE: python/pod5/src/pod5/repack.py
  class Repacker (line 11) | class Repacker:
    method __init__ (line 14) | def __init__(self):
    method is_complete (line 19) | def is_complete(self) -> bool:
    method currently_open_file_reader_count (line 24) | def currently_open_file_reader_count(self) -> int:
    method reads_completed (line 29) | def reads_completed(self) -> int:
    method reads_requested (line 34) | def reads_requested(self) -> int:
    method add_output (line 38) | def add_output(
    method add_selected_reads_to_output (line 64) | def add_selected_reads_to_output(
    method add_all_reads_to_output (line 104) | def add_all_reads_to_output(
    method finish (line 121) | def finish(self) -> None:
    method set_output_finished (line 128) | def set_output_finished(self, output) -> None:

FILE: python/pod5/src/pod5/signal_tools.py
  function vbz_decompress_signal (line 14) | def vbz_decompress_signal(
  function vbz_decompress_signal_chunked (line 39) | def vbz_decompress_signal_chunked(
  function vbz_decompress_signal_into (line 83) | def vbz_decompress_signal_into(
  function vbz_compress_signal (line 109) | def vbz_compress_signal(signal: npt.NDArray[np.int16]) -> npt.NDArray[np...
  function vbz_compress_signal_chunked (line 134) | def vbz_compress_signal_chunked(

FILE: python/pod5/src/pod5/tools/main.py
  function main (line 23) | def main() -> Any:

FILE: python/pod5/src/pod5/tools/parsers.py
  class SubcommandHelpFormatter (line 17) | class SubcommandHelpFormatter(
    method _format_action (line 26) | def _format_action(self, action):
  function run_tool (line 33) | def run_tool(parser: argparse.ArgumentParser) -> Any:
  function add_recursive_argument (line 47) | def add_recursive_argument(parser: argparse.ArgumentParser):
  function add_force_overwrite_argument (line 57) | def add_force_overwrite_argument(parser: argparse._ActionsContainer):
  function pod5_convert_from_fast5_argparser (line 69) | def pod5_convert_from_fast5_argparser(
  function pod5_convert_to_fast5_argparser (line 147) | def pod5_convert_to_fast5_argparser(
  function prepare_pod5_convert (line 204) | def prepare_pod5_convert(parent: argparse._SubParsersAction) -> argparse...
  function prepare_pod5_filter_argparser (line 228) | def prepare_pod5_filter_argparser(
  function prepare_pod5_inspect_argparser (line 294) | def prepare_pod5_inspect_argparser(
  function prepare_pod5_merge_argparser (line 355) | def prepare_pod5_merge_argparser(
  function prepare_pod5_repack_argparser (line 415) | def prepare_pod5_repack_argparser(
  function prepare_pod5_subset_argparser (line 458) | def prepare_pod5_subset_argparser(
  function prepare_pod5_recover_argparser (line 570) | def prepare_pod5_recover_argparser(
  function prepare_pod5_update_argparser (line 610) | def prepare_pod5_update_argparser(
  function prepare_pod5_view_argparser (line 652) | def prepare_pod5_view_argparser(

FILE: python/pod5/src/pod5/tools/pod5_convert_from_fast5.py
  class QueueManager (line 53) | class QueueManager:
    method __init__ (line 54) | def __init__(
    method _await (line 71) | def _await(self, queue: mp.Queue) -> Any:
    method enqueue_request (line 80) | def enqueue_request(self) -> None:
    method await_request (line 83) | def await_request(self) -> None:
    method enqueue_data (line 88) | def enqueue_data(
    method await_data (line 99) | def await_data(
    method enqueue_exception (line 119) | def enqueue_exception(self, path: Path, exception: Exception, trace: s...
    method get_exception (line 122) | def get_exception(self) -> Optional[Tuple[Path, Exception, str]]:
    method enqueue_input (line 137) | def enqueue_input(self, path: Path) -> None:
    method get_input (line 142) | def get_input(self) -> Optional[Path]:
    method _discard_and_close (line 151) | def _discard_and_close(self, queue: mp.Queue) -> int:
    method shutdown (line 168) | def shutdown(self) -> Tuple[int, int, int, int]:
    method _start (line 185) | def _start(self, inputs: Iterable[Path]) -> None:
  class OutputHandler (line 195) | class OutputHandler:
    method __init__ (line 199) | def __init__(
    method _open_writer (line 213) | def _open_writer(self, output_path: Path) -> Optional[p5.Writer]:
    method get_writer (line 232) | def get_writer(self, input_path: Path) -> Optional[p5.Writer]:
    method resolve_one_to_one_path (line 245) | def resolve_one_to_one_path(path: Path, root: Path, relative_root: Path):
    method resolve_output_path (line 263) | def resolve_output_path(
    method set_input_complete (line 291) | def set_input_complete(self, input_path: Path, is_exception: bool) -> ...
    method close_all (line 306) | def close_all(self):
  class StatusMonitor (line 319) | class StatusMonitor:
    method __init__ (line 323) | def __init__(self, paths: Sequence[Path]):
    method total_files (line 337) | def total_files(self) -> int:
    method total_reads (line 341) | def total_reads(self) -> int:
    method increment_reads (line 345) | def increment_reads(self, n: int) -> None:
    method update_reads_total (line 350) | def update_reads_total(self, path: Path, total: int) -> None:
    method write (line 357) | def write(self, msg: str, file: Any) -> None:
    method close (line 362) | def close(self) -> None:
  function is_multi_read_fast5 (line 368) | def is_multi_read_fast5(path: Path) -> bool:
  function decode_str (line 394) | def decode_str(value: Union[str, bytes]) -> str:
  function convert_fast5_end_reason (line 401) | def convert_fast5_end_reason(fast5_end_reason: int) -> p5.EndReason:
  function convert_datetime_as_epoch_ms (line 429) | def convert_datetime_as_epoch_ms(
  function convert_run_info (line 442) | def convert_run_info(
  function convert_fast5_read (line 484) | def convert_fast5_read(
  function get_read_from_fast5 (line 571) | def get_read_from_fast5(group_name: str, h5_file: h5py.File) -> Optional...
  function convert_fast5_file_chunk (line 587) | def convert_fast5_file_chunk(
  function convert_fast5_file (line 614) | def convert_fast5_file(
  function issue_not_multi_read_exception (line 636) | def issue_not_multi_read_exception(path: Path, queues: QueueManager):
  function convert_fast5_files (line 648) | def convert_fast5_files(
  function handle_exception (line 684) | def handle_exception(
  function process_conversion_tasks (line 702) | def process_conversion_tasks(
  function convert_from_fast5 (line 756) | def convert_from_fast5(
  function main (line 834) | def main():

FILE: python/pod5/src/pod5/tools/pod5_convert_to_fast5.py
  class StatusMonitor (line 39) | class StatusMonitor:
    method __init__ (line 42) | def __init__(self, file_count: int):
    method running (line 55) | def running(self) -> bool:
    method increment (line 59) | def increment(
    method samples_mb (line 76) | def samples_mb(self) -> float:
    method time_elapsed (line 81) | def time_elapsed(self) -> float:
    method sample_rate (line 86) | def sample_rate(self) -> float:
    method print_status (line 90) | def print_status(self, force: bool = False):
    method formatted_sample_count (line 105) | def formatted_sample_count(self) -> str:
  function write_pod5_record_to_fast5 (line 120) | def write_pod5_record_to_fast5(read: p5.ReadRecord, fast5: h5py.File) ->...
  function convert_pod5_to_fast5 (line 218) | def convert_pod5_to_fast5(
  function convert_to_fast5 (line 253) | def convert_to_fast5(
  function main (line 317) | def main():

FILE: python/pod5/src/pod5/tools/pod5_filter.py
  function parse_read_id_targets (line 28) | def parse_read_id_targets(ids: Path, output: Path) -> pl.LazyFrame:
  function filter_pod5 (line 57) | def filter_pod5(
  function main (line 107) | def main():

FILE: python/pod5/src/pod5/tools/pod5_inspect.py
  function format_shift_scale_pair (line 18) | def format_shift_scale_pair(pair):
  function format_shift_scale_pair_num (line 22) | def format_shift_scale_pair_num(pair):
  function do_reads_command (line 26) | def do_reads_command(reader: p5.Reader, write_header: bool):
  function dump_run_info (line 82) | def dump_run_info(run_info: p5.RunInfo):
  function do_read_command (line 93) | def do_read_command(reader: p5.Reader, read_id: str, **_):
  function do_debug_command (line 132) | def do_debug_command(reader: p5.Reader, **_):
  function do_summary_command (line 174) | def do_summary_command(reader: p5.Reader, **kwargs):
  function inspect_pod5 (line 199) | def inspect_pod5(
  function main (line 225) | def main():

FILE: python/pod5/src/pod5/tools/pod5_merge.py
  function merge_pod5 (line 25) | def merge_pod5(
  function main (line 104) | def main():

FILE: python/pod5/src/pod5/tools/pod5_recover.py
  class RecoveredData (line 17) | class RecoveredData:
  function is_file_ok (line 28) | def is_file_ok(path: Path) -> bool:
  function recover_pod5 (line 37) | def recover_pod5(
  function main (line 95) | def main():

FILE: python/pod5/src/pod5/tools/pod5_repack.py
  function resolve_overwrite (line 22) | def resolve_overwrite(src: Path, dest: Path, force: bool) -> None:
  function repack_pod5_file (line 34) | def repack_pod5_file(src: Path, dest: Path):
  function repack_pod5 (line 46) | def repack_pod5(
  function main (line 90) | def main():

FILE: python/pod5/src/pod5/tools/pod5_subset.py
  function get_separator (line 36) | def get_separator(path: Path) -> str:
  function default_filename_template (line 52) | def default_filename_template(subset_columns: List[str]) -> str:
  function column_keys_from_template (line 60) | def column_keys_from_template(template: str) -> List[str]:
  function fstring_to_polars (line 66) | def fstring_to_polars(
  function parse_table_mapping (line 82) | def parse_table_mapping(
  function assert_filename_template (line 134) | def assert_filename_template(
  function create_default_filename_template (line 162) | def create_default_filename_template(subset_columns: List[str]) -> str:
  function parse_csv_mapping (line 170) | def parse_csv_mapping(csv_path: Path) -> pl.LazyFrame:
  function build_targets_dict (line 198) | def build_targets_dict(
  function subset_pod5 (line 211) | def subset_pod5(
  function main (line 268) | def main():

FILE: python/pod5/src/pod5/tools/pod5_update.py
  function update_pod5 (line 21) | def update_pod5(
  function main (line 62) | def main():

FILE: python/pod5/src/pod5/tools/pod5_view.py
  class Selection (line 39) | class Selection(NamedTuple):
    method __contains__ (line 44) | def __contains__(self, key):
    method union (line 47) | def union(self) -> Set[str]:
  class Field (line 51) | class Field(NamedTuple):
  function print_fields (line 169) | def print_fields():
  function get_field_or_raise (line 177) | def get_field_or_raise(key: str) -> Field:
  function select_fields (line 189) | def select_fields(
  function get_format_view_table_fn (line 247) | def get_format_view_table_fn(
  function write (line 303) | def write(
  function write_header (line 333) | def write_header(
  function resolve_output (line 345) | def resolve_output(output: Optional[Path], force_overwrite: bool) -> Opt...
  function assert_unique_acquisition_id (line 370) | def assert_unique_acquisition_id(run_info: pl.LazyFrame, path: Path) -> ...
  function parse_reads_table_all (line 382) | def parse_reads_table_all(
  function parse_reads_table_batch (line 400) | def parse_reads_table_batch(
  function parse_read_table_chunks (line 423) | def parse_read_table_chunks(
  function parse_run_info_table (line 454) | def parse_run_info_table(
  function join_reads_to_run_info (line 479) | def join_reads_to_run_info(reads: pl.LazyFrame, run_info: pl.LazyFrame) ...
  function get_included_reads_table_fields (line 488) | def get_included_reads_table_fields(reader: p5.Reader, selection: Select...
  function get_reads_tables (line 501) | def get_reads_tables(
  function join_workers (line 535) | def join_workers(processes: List[SpawnProcess], exceptions: mp.JoinableQ...
  function worker_process (line 572) | def worker_process(
  function launch_view_workers (line 605) | def launch_view_workers(
  function view_pod5 (line 649) | def view_pod5(
  function main (line 696) | def main():

FILE: python/pod5/src/pod5/tools/polars_utils.py
  function pl_format_read_id (line 12) | def pl_format_read_id(read_id_col: pl.Expr) -> pl.Expr:
  function pl_format_empty_string (line 25) | def pl_format_empty_string(expr: pl.Expr, subst: Optional[str]) -> pl.Expr:
  function pl_from_arrow (line 30) | def pl_from_arrow(table: pa.Table, rechunk: bool) -> pl.DataFrame:
  function pl_from_arrow_batch (line 51) | def pl_from_arrow_batch(record_batch: pa.RecordBatch, rechunk: bool) -> ...

FILE: python/pod5/src/pod5/tools/utils.py
  function init_logging (line 22) | def init_logging():
  function logged (line 46) | def logged(log_return: bool = False, log_args: bool = False, log_time: b...
  function terminate_processes (line 80) | def terminate_processes(processes: List[SpawnProcess]) -> None:
  function limit_threads (line 92) | def limit_threads(requested: int) -> int:
  function collect_inputs (line 102) | def collect_inputs(
  function assert_inputs_exist (line 125) | def assert_inputs_exist(inputs: Iterable[Path]):
  function search_paths (line 137) | def search_paths(
  function search_path (line 161) | def search_path(path: Path, recursive: bool, patterns: Collection[str]) ...
  function assert_no_duplicate_filenames (line 186) | def assert_no_duplicate_filenames(inputs: Collection[Path]) -> None:
  function is_disable_pbar (line 199) | def is_disable_pbar() -> bool:
  function is_pod5_debug (line 217) | def is_pod5_debug() -> bool:

FILE: python/pod5/src/pod5/writer.py
  function force_type_and_default (line 51) | def force_type_and_default(value, dtype, count, default_value=None):
  function map_to_tuples (line 58) | def map_to_tuples(info_map: Any) -> List[Tuple[str, str]]:
  function timestamp_to_int (line 70) | def timestamp_to_int(time_stamp: Union[datetime.datetime, int]) -> int:
  class Writer (line 77) | class Writer:
    method __init__ (line 80) | def __init__(
    method __enter__ (line 136) | def __enter__(self) -> "Writer":
    method __exit__ (line 139) | def __exit__(self, *exc_details) -> None:
    method close (line 142) | def close(self) -> None:
    method path (line 148) | def path(self) -> Path:
    method software_name (line 153) | def software_name(self) -> str:
    method signal_compression_type (line 158) | def signal_compression_type(self) -> SignalType:
    method add (line 162) | def add(self, obj: Union[EndReason, PoreType, RunInfo]) -> int:
    method _add_end_reason (line 193) | def _add_end_reason(self, end_reason: EndReason) -> int:
    method _add_pore_type (line 199) | def _add_pore_type(self, pore_type: PoreType) -> int:
    method _add_run_info (line 205) | def _add_run_info(self, run_info: RunInfo) -> int:
    method contains (line 233) | def contains(self, obj: Union[EndReason, RunInfo]) -> bool:
    method find (line 249) | def find(self, obj: Union[EndReason, RunInfo]) -> int:
    method add_read (line 275) | def add_read(self, read: Union[Read, CompressedRead]) -> None:
    method add_reads (line 287) | def add_reads(self, reads: Sequence[Union[Read, CompressedRead]]) -> N...
    method _prepare_add_reads_args (line 334) | def _prepare_add_reads_args(self, reads: Sequence[BaseRead]) -> List[A...

FILE: python/pod5/src/tests/conftest.py
  function pytest_addoption (line 35) | def pytest_addoption(parser):
  function assert_no_leaked_handles (line 46) | def assert_no_leaked_handles() -> Generator[None, None, None]:
  function assert_no_leaked_handles_win (line 57) | def assert_no_leaked_handles_win(path: Path) -> None:
  function reader (line 68) | def reader() -> Generator[p5.Reader, None, None]:
  function writer (line 77) | def writer(tmp_path: Path) -> Generator[p5.Writer, None, None]:
  function rand_float (line 90) | def rand_float(seed: int) -> float:
  function rand_int (line 96) | def rand_int(low: int, high: int, seed: int) -> int:
  function rand_str (line 102) | def rand_str(prefix: str, seed: int) -> str:
  function _random_read_id (line 108) | def _random_read_id(seed: int = 1) -> UUID:
  function random_read_id (line 114) | def random_read_id(request) -> UUID:
  function _random_pore (line 119) | def _random_pore(seed: int) -> p5.Pore:
  function random_pore (line 127) | def random_pore(request) -> p5.Pore:
  function _random_calibration (line 132) | def _random_calibration(seed: int = 1) -> p5.Calibration:
  function random_calibration (line 138) | def random_calibration(request) -> p5.Calibration:
  function _random_end_reason (line 143) | def _random_end_reason(seed: int = 1) -> p5.EndReason:
  function random_end_reason (line 151) | def random_end_reason(request) -> p5.EndReason:
  function _random_run_info (line 156) | def _random_run_info(seed: int = 1) -> p5.RunInfo:
  function random_run_info (line 185) | def random_run_info(request) -> p5.RunInfo:
  function _random_signal (line 190) | def _random_signal(seed: int = 1) -> numpy.typing.NDArray[numpy.int16]:
  function random_signal (line 198) | def random_signal(request) -> numpy.typing.NDArray[numpy.int16]:
  function _random_read (line 203) | def _random_read(seed: int = 1) -> p5.Read:
  function random_read (line 222) | def random_read(request) -> p5.Read:
  function _random_read_pre_compressed (line 227) | def _random_read_pre_compressed(seed: int = 1) -> p5.CompressedRead:
  function random_read_pre_compressed (line 247) | def random_read_pre_compressed(request) -> p5.CompressedRead:
  function _seeder (line 252) | def _seeder(seed: int) -> Generator[int, None, None]:
  function pod5_factory (line 262) | def pod5_factory(request, tmp_path_factory: pytest.TempPathFactory, pyte...
  function nested_dataset (line 313) | def nested_dataset(tmp_path_factory: pytest.TempPathFactory, pod5_factor...

FILE: python/pod5/src/tests/test_api.py
  function gen_test_read (line 17) | def gen_test_read(seed, compressed=False) -> Union[p5.Read, p5.Compresse...
  function run_writer_test (line 88) | def run_writer_test(f: Writer):
  function run_reader_test (line 118) | def run_reader_test(reader: p5.Reader):
  function test_pyarrow_from_pathlib (line 233) | def test_pyarrow_from_pathlib():
  function test_pyarrow_from_str (line 244) | def test_pyarrow_from_str():
  function test_pyarrow_from_pathlib_uncompressed (line 255) | def test_pyarrow_from_pathlib_uncompressed():
  function test_read_id_packing (line 267) | def test_read_id_packing():

FILE: python/pod5/src/tests/test_convert_from_fast5.py
  function unraisablehook (line 211) | def unraisablehook(unraisable):
  class TestFast5Conversion (line 218) | class TestFast5Conversion:
    method test_convert_fast5_read (line 221) | def test_convert_fast5_read(self) -> None:
    method test_end_reason (line 258) | def test_end_reason(self, fast5: int, expected: pod5.EndReasonEnum) ->...
    method test_convert_run_info_defaults (line 262) | def test_convert_run_info_defaults(self) -> None:
    method test_convert_run_info (line 296) | def test_convert_run_info(self) -> None:
  class TestFast5Detection (line 349) | class TestFast5Detection:
    method test_single_read_fast5_detection (line 350) | def test_single_read_fast5_detection(self):
    method test_multi_read_fast5_detection (line 354) | def test_multi_read_fast5_detection(self):
    method test_read_id_keys_detected (line 358) | def test_read_id_keys_detected(self) -> None:
    method test_unknown_keys_ignored (line 364) | def test_unknown_keys_ignored(self) -> None:
    method test_bad_keys_skipped_with_warning (line 369) | def test_bad_keys_skipped_with_warning(self) -> None:
  class TestConvertBehaviour (line 377) | class TestConvertBehaviour:
    method test_no_unforced_overwrite (line 380) | def test_no_unforced_overwrite(self, tmp_path: Path):
    method test_forced_overwrite (line 388) | def test_forced_overwrite(self, tmp_path: Path):
    method test_directory_output (line 395) | def test_directory_output(self, tmp_path: Path):
    method test_single_file_output (line 406) | def test_single_file_output(self, tmp_path: Path):
    method test_output_121_relative (line 415) | def test_output_121_relative(self, tmp_path: Path):
    method test_output_121_relative_no_parents (line 440) | def test_output_121_relative_no_parents(self, tmp_path: Path):
  class TestOutputHandler (line 465) | class TestOutputHandler:
    method test_output_handler_default_writer (line 466) | def test_output_handler_default_writer(self, tmp_path: Path):
    method test_output_handler_one_to_one_writer (line 479) | def test_output_handler_one_to_one_writer(self, tmp_path: Path):
    method test_output_handler_one_to_one_multiple_writer (line 492) | def test_output_handler_one_to_one_multiple_writer(self, tmp_path: Path):
    method test_no_reopen (line 506) | def test_no_reopen(self, tmp_path: Path):
    method test_none_if_exception (line 515) | def test_none_if_exception(self, tmp_path: Path):
    method test_no_duplicate_open (line 523) | def test_no_duplicate_open(self, tmp_path: Path):
  class TestQueueManager (line 532) | class TestQueueManager:
    method test_shutdown (line 533) | def test_shutdown(self, monkeypatch, caplog: pytest.LogCaptureFixture):
    method test_shutdown_with_work (line 558) | def test_shutdown_with_work(self, monkeypatch, caplog: pytest.LogCaptu...
    method test_blocked_by_requests (line 587) | def test_blocked_by_requests(self) -> None:
    method test_data_queue (line 606) | def test_data_queue(self) -> None:
    method test_exception_queue (line 634) | def test_exception_queue(self) -> None:
  class TestConvertLoop (line 656) | class TestConvertLoop:
    method test_convert_fast5_files_file_type_exceptions (line 657) | def test_convert_fast5_files_file_type_exceptions(self, tmp_path: Path...
    method test_convert_fast5_files_breaks_loop (line 674) | def test_convert_fast5_files_breaks_loop(self) -> None:
    method test_convert_fast5_file_exception (line 691) | def test_convert_fast5_file_exception(self, mock: Mock) -> None:
    method test_handle_exception (line 710) | def test_handle_exception(self) -> None:

FILE: python/pod5/src/tests/test_convert_to_fast5.py
  class TestPod5ConversionRoundTrip (line 19) | class TestPod5ConversionRoundTrip:
    method test_convert_pod5_to_fast5_and_back (line 22) | def test_convert_pod5_to_fast5_and_back(self, tmp_path: Path) -> None:
  class TestConvertBehaviour (line 74) | class TestConvertBehaviour:
    method test_no_unforced_overwrite (line 77) | def test_no_unforced_overwrite(self, tmp_path: Path):
    method test_forced_overwrite (line 85) | def test_forced_overwrite(self, tmp_path: Path):
    method test_recursive_input (line 96) | def test_recursive_input(self, tmp_path: Path):
    method test_multiple_outputs (line 107) | def test_multiple_outputs(self, tmp_path: Path):

FILE: python/pod5/src/tests/test_dataset.py
  class TestDatasetReader (line 39) | class TestDatasetReader:
    method test_bad_file_num_reads (line 44) | def test_bad_file_num_reads(self, tmp_path: Path) -> None:
    method test_len_single (line 52) | def test_len_single(self) -> None:
    method test_iter_single (line 59) | def test_iter_single(self) -> None:
    method test_no_recursive (line 66) | def test_no_recursive(self, nested_dataset: Path) -> None:
    method test_recursive (line 80) | def test_recursive(self, nested_dataset: Path) -> None:
    method test_get_reader_is_cached (line 107) | def test_get_reader_is_cached(self, nested_dataset: Path) -> None:
    method test_reader_all_cache (line 120) | def test_reader_all_cache(self, nested_dataset: Path) -> None:
    method test_reader_all_cache_context (line 139) | def test_reader_all_cache_context(self, nested_dataset: Path) -> None:
    method test_reader_no_cache (line 157) | def test_reader_no_cache(self, nested_dataset: Path) -> None:
    method test_reader_clear_readers (line 176) | def test_reader_clear_readers(self, nested_dataset: Path) -> None:
    method test_reader_cache_delete (line 195) | def test_reader_cache_delete(self, nested_dataset: Path) -> None:
    method test_random_read_indexing (line 213) | def test_random_read_indexing(self, nested_dataset: Path) -> None:
    method test_duplicate_read_selection (line 229) | def test_duplicate_read_selection(self, nested_dataset: Path) -> None:
    method test_missing_id_does_not_return_member (line 245) | def test_missing_id_does_not_return_member(self, nested_dataset: Path)...
    method test_invalid_id_does_not_return_member (line 271) | def test_invalid_id_does_not_return_member(self, nested_dataset: Path)...
    method test_empty_read_selection (line 291) | def test_empty_read_selection(self, nested_dataset: Path) -> None:
    method test_prompt_read_indexing (line 297) | def test_prompt_read_indexing(self, nested_dataset: Path) -> None:
    method test_iter_multi (line 304) | def test_iter_multi(self, nested_dataset: Path) -> None:
    method test_iter_multi_single_thread (line 317) | def test_iter_multi_single_thread(self, nested_dataset: Path) -> None:
    method test_iter_multi_multi_thread (line 335) | def test_iter_multi_multi_thread(self, nested_dataset: Path) -> None:
    method test_iter_multi_multi_thread_no_cache (line 351) | def test_iter_multi_multi_thread_no_cache(self, nested_dataset: Path) ...
    method test_mixed_load (line 372) | def test_mixed_load(self, nested_dataset: Path) -> None:
    method test_iter_selection (line 380) | def test_iter_selection(self, nested_dataset: Path) -> None:
    method test_iter_duplicate (line 393) | def test_iter_duplicate(self, nested_dataset: Path) -> None:
    method test_duplicate (line 409) | def test_duplicate(self, tmp_path: Path) -> None:
    method test_duplicate_index_warns (line 424) | def test_duplicate_index_warns(self, tmp_path: Path) -> None:
    method test_iter_missing (line 443) | def test_iter_missing(self, nested_dataset: Path) -> None:
    method test_get_path (line 458) | def test_get_path(self, nested_dataset: Path) -> None:
    method test_collect_paths (line 468) | def test_collect_paths(self, nested_dataset: Path) -> None:

FILE: python/pod5/src/tests/test_filter.py
  class TestFilterParseIds (line 27) | class TestFilterParseIds:
    method _read_ids_path (line 30) | def _read_ids_path(self, tmp_path: Path, ids: List[str]) -> Path:
    method _assert_columns (line 35) | def _assert_columns(self, df: pl.LazyFrame) -> None:
    method _assert_all_expected (line 39) | def _assert_all_expected(self, df: pl.LazyFrame) -> None:
    method test_example (line 45) | def test_example(self, tmp_path: Path) -> None:
    method test_example_with_header (line 53) | def test_example_with_header(self, tmp_path: Path) -> None:
    method test_example_with_comments (line 64) | def test_example_with_comments(self, tmp_path: Path) -> None:
    method test_example_with_whitespace (line 76) | def test_example_with_whitespace(self, tmp_path: Path) -> None:
    method test_no_ids (line 88) | def test_no_ids(self, tmp_path: Path) -> None:
  class TestFilter (line 98) | class TestFilter:
    method test_all_in_out (line 99) | def test_all_in_out(self, tmp_path: Path) -> None:
    method test_no_duplicates (line 131) | def test_no_duplicates(self, tmp_path: Path) -> None:
    method test_missing_read_ids (line 161) | def test_missing_read_ids(self, tmp_path: Path) -> None:
    method test_force_overwrite (line 194) | def test_force_overwrite(self, tmp_path: Path) -> None:
    method test_empty_input_fails (line 222) | def test_empty_input_fails(self, tmp_path: Path) -> None:
    method test_random_inputs (line 240) | def test_random_inputs(self, pod5_factory, tmp_path: Path, n_reads: in...
    method test_input_directory (line 266) | def test_input_directory(self, tmp_path: Path) -> None:
    method test_recursive_inputs_symlink (line 286) | def test_recursive_inputs_symlink(self, tmp_path: Path) -> None:

FILE: python/pod5/src/tests/test_inspect.py
  class TestReads (line 11) | class TestReads:
    method test_reads_header_written_once (line 12) | def test_reads_header_written_once(

FILE: python/pod5/src/tests/test_merge.py
  class TestMerge (line 11) | class TestMerge:
    method test_merge_runs (line 14) | def test_merge_runs(self, tmp_path: Path):
    method test_merge_duplicate_stopped (line 33) | def test_merge_duplicate_stopped(self, tmp_path: Path):

FILE: python/pod5/src/tests/test_reader.py
  class TestPod5Reader (line 25) | class TestPod5Reader:
    method test_reader_fixture (line 28) | def test_reader_fixture(self, reader: p5.Reader) -> None:
    method test_reader_reads_types (line 52) | def test_reader_reads_types(
    method test_reader_reads_numpy_types (line 73) | def test_reader_reads_numpy_types(
    method test_reader_reads_container_types (line 100) | def test_reader_reads_container_types(
    method test_attribute_types (line 122) | def test_attribute_types(self) -> None:
    method test_without_mmap (line 152) | def test_without_mmap(self) -> None:
    method test_sparse_file_warns_during_preflight (line 169) | def test_sparse_file_warns_during_preflight(self, tmp_path: Path, capf...
    method test_iter_selection_in_file_order (line 197) | def test_iter_selection_in_file_order(self, reader: p5.Reader) -> None:
  class TestRecordBatch (line 208) | class TestRecordBatch:
    method test_get_read (line 209) | def test_get_read(self, pod5_factory) -> None:
    method test_column_selection (line 223) | def test_column_selection(self, pod5_factory) -> None:
    method test_read_batches (line 248) | def test_read_batches(self, pod5_factory) -> None:
    method test_read_batches_raises (line 257) | def test_read_batches_raises(self, pod5_factory) -> None:
    method test_cache_exceptions (line 269) | def test_cache_exceptions(self, pod5_factory) -> None:

FILE: python/pod5/src/tests/test_recover.py
  class TestRecover (line 17) | class TestRecover:
    method _generate_recoverable_file (line 20) | def _generate_recoverable_file(self, dest_path: Path, read_count=1200):
    method test_recover_runs (line 40) | def test_recover_runs(

FILE: python/pod5/src/tests/test_repack.py
  class TestRepack (line 17) | class TestRepack:
    method test_works (line 20) | def test_works(self, tmp_path: Path) -> None:
    method test_detect_name_collision (line 41) | def test_detect_name_collision(self, tmp_path: Path) -> None:
    method test_overwrite_symlink (line 56) | def test_overwrite_symlink(self, tmp_path: Path) -> None:
    method test_overwrite_data (line 85) | def test_overwrite_data(self, tmp_path: Path) -> None:
  class TestRepacker (line 106) | class TestRepacker:
    method test_add_all (line 107) | def test_add_all(self, tmp_path: Path, pod5_factory) -> None:
    method test_add_selection (line 130) | def test_add_selection(self, tmp_path: Path, pod5_factory) -> None:
    method test_missing_selection (line 154) | def test_missing_selection(self, tmp_path: Path, pod5_factory) -> None:

FILE: python/pod5/src/tests/test_signal_tools.py
  class TestPod5SignalTools (line 24) | class TestPod5SignalTools:
    method test_round_trip (line 28) | def test_round_trip(self, random_signal: npt.NDArray[np.int16]) -> None:
    method test_round_trip_empty (line 37) | def test_round_trip_empty(self) -> None:
    method test_round_trip_chunked (line 47) | def test_round_trip_chunked(self, random_signal: npt.NDArray[np.int16]...
    method test_round_trip_chunked_empty (line 66) | def test_round_trip_chunked_empty(self) -> None:
  class DemoObj (line 86) | class DemoObj:
    method __init__ (line 87) | def __init__(self, path: Path) -> None:
    method __del__ (line 91) | def __del__(self):
  function demo_obj (line 96) | def demo_obj(tmp_path: Path) -> DemoObj:
  class TestSafeClose (line 102) | class TestSafeClose:
    method test_closes (line 105) | def test_closes(self, demo_obj: DemoObj) -> None:
    method test_passes_unknown_attribute (line 111) | def test_passes_unknown_attribute(self, demo_obj: DemoObj) -> None:
    method test_passes_known_non_handle_attribute (line 116) | def test_passes_known_non_handle_attribute(self, demo_obj: DemoObj) ->...

FILE: python/pod5/src/tests/test_subset.py
  function get_resource_module (line 29) | def get_resource_module() -> ModuleType | None:
  class TestSubset (line 91) | class TestSubset:
    method csv_mapping_single (line 95) | def csv_mapping_single(path: Path, mapping: Dict[str, Set[str]]) -> Path:
    method _test_subset (line 104) | def _test_subset(self, tmp: Path, csv: Path, mapping: Dict[str, Set[st...
    method test_subset_base (line 132) | def test_subset_base(self, tmp_path: Path):
    method test_subset_shared_read_id (line 137) | def test_subset_shared_read_id(self, tmp_path: Path):
    method test_subset_duplicate_read_id (line 142) | def test_subset_duplicate_read_id(self, tmp_path: Path):
    method test_subset_dir_and_recurse (line 147) | def test_subset_dir_and_recurse(
    method test_assert_overwrite (line 180) | def test_assert_overwrite(self, tmp_path: Path) -> None:
    method _pod5s_with_view_table (line 190) | def _pod5s_with_view_table(
    method test_subset_ulimit_below_num_outputs (line 214) | def test_subset_ulimit_below_num_outputs(
    method test_subset_ulimit_below_num_inputs (line 262) | def test_subset_ulimit_below_num_inputs(
  class TestFilenameTemplating (line 307) | class TestFilenameTemplating:
    method test_default_template (line 318) | def test_default_template(self, columns: List[str], expected: str):
    method test_column_keys_from_template (line 336) | def test_column_keys_from_template(self, keys: List[str], template: st...
    method test_fstring_to_polars (line 353) | def test_fstring_to_polars(
    method test_template_assertions (line 360) | def test_template_assertions(self) -> None:
  class TestParse (line 373) | class TestParse:
    method test_csv_separator (line 374) | def test_csv_separator(self, tmp_path: Path) -> None:
    method test_tsv_separator (line 380) | def test_tsv_separator(self, tmp_path: Path) -> None:
    method _inspect_reads_content (line 386) | def _inspect_reads_content(
    method _write_csv (line 392) | def _write_csv(self, tmp_path: Path, content: str) -> Path:
    method _write_tsv (line 398) | def _write_tsv(self, tmp_path: Path, content: str) -> Path:
    method test_csv_tsv_parse_equal_1 (line 405) | def test_csv_tsv_parse_equal_1(
    method test_csv_tsv_parse_equal_2 (line 462) | def test_csv_tsv_parse_equal_2(
    method test_parse_csv_filters_invalid_read_ids (line 516) | def test_parse_csv_filters_invalid_read_ids(self, tmp_path: Path) -> N...
    method test_parse_table_filters_invalid_read_ids (line 532) | def test_parse_table_filters_invalid_read_ids(self, tmp_path: Path) ->...

FILE: python/pod5/src/tests/test_tools.py
  function assert_exit_code (line 30) | def assert_exit_code(func: Callable, func_kwargs: Dict, exit_code: int =...
  class TestPod5Tools (line 38) | class TestPod5Tools:
    method test_main_calls_run (line 42) | def test_main_calls_run(self, m_run_tool: Mock) -> None:
    method test_run_tool_debug_env (line 49) | def test_run_tool_debug_env(
    method test_run_tool_raises (line 72) | def test_run_tool_raises(self, monkeypatch: pytest.MonkeyPatch) -> None:
    method test_pod5_version_argument (line 90) | def test_pod5_version_argument(self, capsys: pytest.CaptureFixture) ->...
    method test_convert_exists (line 98) | def test_convert_exists(self, subcommand: str) -> None:
    method test_inspect_exists (line 105) | def test_inspect_exists(self, subcommand: str) -> None:
    method test_tool_exists (line 115) | def test_tool_exists(self, command: str) -> None:
    method test_convert_from_fast5_runs (line 121) | def test_convert_from_fast5_runs(self, tmp_path: Path) -> None:
    method test_convert_to_fast5_runs (line 136) | def test_convert_to_fast5_runs(self, tmp_path: Path) -> None:
    method test_inspect_command_runs (line 163) | def test_inspect_command_runs(self, tmp_path: Path, subcommand: str) -...
    method test_inspect_read_finds_read (line 175) | def test_inspect_read_finds_read(self, capsys: pytest.CaptureFixture) ...
    method test_merge_command_runs (line 196) | def test_merge_command_runs(self, tmp_path: Path) -> None:
    method test_repack_command_runs (line 209) | def test_repack_command_runs(self, tmp_path: Path) -> None:
    method test_recover_command_runs (line 222) | def test_recover_command_runs(self) -> None:
    method test_subset_command_runs (line 233) | def test_subset_command_runs(self, tmp_path: Path) -> None:
    method test_filter_command_runs (line 252) | def test_filter_command_runs(self, tmp_path: Path) -> None:
    method test_update_command_runs (line 267) | def test_update_command_runs(self, tmp_path: Path) -> None:
    method test_view_command_runs (line 280) | def test_view_command_runs(self) -> None:
    method test_view_command_runs_list_fields (line 291) | def test_view_command_runs_list_fields(self) -> None:
    method test_scripts_run_directly (line 309) | def test_scripts_run_directly(self, script: Path) -> None:
  class TestUtils (line 315) | class TestUtils:
    method test_collect_inputs (line 316) | def test_collect_inputs(self, tmp_path: Path) -> None:
    method test_collect_inputs_non_existent (line 366) | def test_collect_inputs_non_existent(self, tmp_path: Path) -> None:
    method test_limit_threads (line 372) | def test_limit_threads(self) -> None:

FILE: python/pod5/src/tests/test_update.py
  class TestUpdate (line 14) | class TestUpdate:
    method test_detect_inplace_update (line 17) | def test_detect_inplace_update(self, tmp_path: Path) -> None:
    method test_update (line 25) | def test_update(self, tmp_path: Path) -> None:

FILE: python/pod5/src/tests/test_view.py
  class TestView (line 60) | class TestView:
    method is_equal_or_not_set (line 63) | def is_equal_or_not_set(self, field: str, expected: str) -> None:
    method _compare (line 66) | def _compare(self, record: p5.ReadRecord, row: Dict[str, Any]) -> None:
    method test_view (line 102) | def test_view(self, tmp_path: Path):
    method test_view_no_input (line 130) | def test_view_no_input(self, tmp_path: Path):
    method test_write_stdout (line 135) | def test_write_stdout(self, capsys: pytest.CaptureFixture) -> None:
    method test_is_loadable (line 151) | def test_is_loadable(self, tmp_path: Path) -> None:
    method test_parse_run_info (line 163) | def test_parse_run_info(self, pod5_factory) -> None:
    method test_parse_reads_all (line 180) | def test_parse_reads_all(self, pod5_factory) -> None:
    method test_parse_reads_multi_chunk (line 198) | def test_parse_reads_multi_chunk(self, pod5_factory) -> None:
    method test_unique_on_duplicated_run_info (line 223) | def test_unique_on_duplicated_run_info(self) -> None:
  class TestSelection (line 241) | class TestSelection:
    method test_select (line 244) | def test_select(self) -> None:
    method test_misspelling (line 276) | def test_misspelling(self, field: str) -> None:
    method test_randomly (line 281) | def test_randomly(self) -> None:
    method test_get_field (line 298) | def test_get_field(self) -> None:
  class TestMisc (line 311) | class TestMisc:
    method test_resolve_output (line 312) | def test_resolve_output(self, tmp_path: Path) -> None:
    method test_fields (line 331) | def test_fields(self) -> None:
    method test_unique_acquisition_id (line 335) | def test_unique_acquisition_id(self) -> None:

FILE: python/pod5/src/tests/test_writer.py
  class TestPod5Writer (line 13) | class TestPod5Writer:
    method test_writer_fixture (line 16) | def test_writer_fixture(self, writer: p5.Writer) -> None:
    method test_writer_random_reads (line 22) | def test_writer_random_reads(self, writer: p5.Writer, random_read: p5....
    method test_writer_random_reads_compressed (line 28) | def test_writer_random_reads_compressed(
    method test_read_edit_write (line 34) | def test_read_edit_write(self, reader: p5.Reader, writer: p5.Writer) -...
    method test_read_copy (line 72) | def test_read_copy(self, reader: p5.Reader, writer: p5.Writer) -> None:
    method test_read_record_type_check (line 118) | def test_read_record_type_check(self, reader: p5.Reader, writer: p5.Wr...

FILE: python/pod5/test_utils/check_pod5_files_equal.py
  function main (line 9) | def main():

FILE: test_package/conanfile.py
  class TestPackageConan (line 8) | class TestPackageConan(ConanFile):
    method requirements (line 22) | def requirements(self):
    method layout (line 25) | def layout(self):
    method build (line 28) | def build(self):
    method _test_executable (line 34) | def _test_executable(self):
    method test (line 37) | def test(self):

FILE: test_package/test_package.cpp
  function main (line 5) | int main()

FILE: third_party/include/catch2/catch.hpp
  type Catch (line 97) | namespace Catch {
    type CaseSensitive (line 514) | struct CaseSensitive {
      type Choice (line 515) | enum Choice { Yes, No }
    class NonCopyable (line 518) | class NonCopyable {
      method NonCopyable (line 519) | NonCopyable(NonCopyable const &) = delete;
      method NonCopyable (line 520) | NonCopyable(NonCopyable &&) = delete;
      method NonCopyable (line 521) | NonCopyable &operator=(NonCopyable const &) = delete;
      method NonCopyable (line 522) | NonCopyable &operator=(NonCopyable &&) = delete;
    type SourceLineInfo (line 529) | struct SourceLineInfo {
      method SourceLineInfo (line 530) | SourceLineInfo() = delete;
      method SourceLineInfo (line 531) | SourceLineInfo(char const *_file, std::size_t _line) noexcept : file...
      method SourceLineInfo (line 533) | SourceLineInfo(SourceLineInfo const &other) = default;
      method SourceLineInfo (line 534) | SourceLineInfo &operator=(SourceLineInfo const &) = default;
      method SourceLineInfo (line 535) | SourceLineInfo(SourceLineInfo &&) noexcept = default;
      method SourceLineInfo (line 536) | SourceLineInfo &operator=(SourceLineInfo &&) noexcept = default;
      method empty (line 538) | bool empty() const noexcept { return file[0] == '\0'; }
    type StreamEndStop (line 557) | struct StreamEndStop {
    function T (line 561) | T const &operator+(T const &value, StreamEndStop) {
    type RegistrarForTagAliases (line 572) | struct RegistrarForTagAliases {
    class TestSpec (line 596) | class TestSpec
      class Pattern (line 5521) | class Pattern {
      class NamePattern (line 5533) | class NamePattern : public Pattern {
      class TagPattern (line 5542) | class TagPattern : public Pattern {
      class ExcludedPattern (line 5551) | class ExcludedPattern : public Pattern {
      type Filter (line 5560) | struct Filter {
      type FilterMatch (line 5568) | struct FilterMatch {
    type ITestInvoker (line 598) | struct ITestInvoker {
    class TestCase (line 603) | class TestCase
    type IConfig (line 604) | struct IConfig
    type ITestCaseRegistry (line 606) | struct ITestCaseRegistry {
    class StringRef (line 634) | class StringRef {
      method StringRef (line 646) | constexpr StringRef() noexcept = default;
      method StringRef (line 650) | constexpr StringRef(char const *rawChars, size_type size) noexcept
      method StringRef (line 653) | StringRef(std::string const &stdString) noexcept
      method empty (line 668) | constexpr auto empty() const noexcept -> bool { return m_size == 0; }
      method size (line 669) | constexpr auto size() const noexcept -> size_type { return m_size; }
      method isNullTerminated (line 684) | constexpr auto isNullTerminated() const noexcept -> bool { return m_...
      method const_iterator (line 687) | constexpr const_iterator begin() const { return m_start; }
      method const_iterator (line 688) | constexpr const_iterator end() const { return m_start + m_size; }
    type always_false (line 1150) | struct always_false : std::false_type {}
    type true_given (line 1153) | struct true_given : std::true_type {}
    type is_callable_tester (line 1154) | struct is_callable_tester {
    type is_callable (line 1162) | struct is_callable
    class TestInvokerAsMethod (line 1190) | class TestInvokerAsMethod : public ITestInvoker {
      method TestInvokerAsMethod (line 1194) | TestInvokerAsMethod(void (C::*testAsMethod)()) noexcept : m_testAsMe...
      method invoke (line 1196) | void invoke() const override {
    function makeTestInvoker (line 1205) | auto makeTestInvoker(void (C::*testAsMethod)()) noexcept -> ITestInvok...
    type NameAndTags (line 1209) | struct NameAndTags {
    type AutoReg (line 1216) | struct AutoReg : NonCopyable {
    type ResultWas (line 1784) | struct ResultWas {
      type OfType (line 1785) | enum OfType {
    type ResultDisposition (line 1810) | struct ResultDisposition {
      type Flags (line 1811) | enum Flags {
    function isFalseTest (line 1823) | inline bool isFalseTest(int flags) { return (flags & ResultDisposition...
    type AssertionInfo (line 1831) | struct AssertionInfo {
    class StringRef (line 1865) | class StringRef
      method StringRef (line 646) | constexpr StringRef() noexcept = default;
      method StringRef (line 650) | constexpr StringRef(char const *rawChars, size_type size) noexcept
      method StringRef (line 653) | StringRef(std::string const &stdString) noexcept
      method empty (line 668) | constexpr auto empty() const noexcept -> bool { return m_size == 0; }
      method size (line 669) | constexpr auto size() const noexcept -> size_type { return m_size; }
      method isNullTerminated (line 684) | constexpr auto isNullTerminated() const noexcept -> bool { return m_...
      method const_iterator (line 687) | constexpr const_iterator begin() const { return m_start; }
      method const_iterator (line 688) | constexpr const_iterator end() const { return m_start + m_size; }
    type IStream (line 1867) | struct IStream {
    class ReusableStringStream (line 1874) | class ReusableStringStream : NonCopyable {
      method get (line 1889) | auto get() -> std::ostream & { return *m_oss; }
    type Detail (line 1900) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type IMutableEnumValuesRegistry (line 1911) | struct IMutableEnumValuesRegistry {
    type Detail (line 1990) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type StringMaker (line 2052) | struct StringMaker {
      method convert (line 2054) | static typename std::enable_if<::Catch::Detail::IsStreamInsertable<F...
      method convert (line 2065) | static typename std::enable_if<!::Catch::Detail::IsStreamInsertable<...
    type Detail (line 2076) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type StringMaker<std::string> (line 2103) | struct StringMaker<std::string> {
    type StringMaker<std::string_view> (line 2109) | struct StringMaker<std::string_view> {
    type StringMaker<char const *> (line 2115) | struct StringMaker<char const *> {
    type StringMaker<char *> (line 2119) | struct StringMaker<char *> {
    type StringMaker<std::wstring> (line 2125) | struct StringMaker<std::wstring> {
    type StringMaker<std::wstring_view> (line 2131) | struct StringMaker<std::wstring_view> {
    type StringMaker<wchar_t const *> (line 2137) | struct StringMaker<wchar_t const *> {
    type StringMaker<wchar_t *> (line 2141) | struct StringMaker<wchar_t *> {
    type StringMaker<char[SZ]> (line 2149) | struct StringMaker<char[SZ]> {
      method convert (line 2150) | static std::string convert(char const *str) {
    type StringMaker<signed char[SZ]> (line 2155) | struct StringMaker<signed char[SZ]> {
      method convert (line 2156) | static std::string convert(signed char const *str) {
    type StringMaker<unsigned char[SZ]> (line 2161) | struct StringMaker<unsigned char[SZ]> {
      method convert (line 2162) | static std::string convert(unsigned char const *str) {
    type StringMaker<std::byte> (line 2169) | struct StringMaker<std::byte> {
    type StringMaker<int> (line 2174) | struct StringMaker<int> {
    type StringMaker<long> (line 2178) | struct StringMaker<long> {
    type StringMaker<long long> (line 2182) | struct StringMaker<long long> {
    type StringMaker<unsigned int> (line 2186) | struct StringMaker<unsigned int> {
    type StringMaker<unsigned long> (line 2190) | struct StringMaker<unsigned long> {
    type StringMaker<unsigned long long> (line 2194) | struct StringMaker<unsigned long long> {
    type StringMaker<bool> (line 2199) | struct StringMaker<bool> {
    type StringMaker<char> (line 2204) | struct StringMaker<char> {
    type StringMaker<signed char> (line 2208) | struct StringMaker<signed char> {
    type StringMaker<unsigned char> (line 2212) | struct StringMaker<unsigned char> {
    type StringMaker<std::nullptr_t> (line 2217) | struct StringMaker<std::nullptr_t> {
    type StringMaker<float> (line 2222) | struct StringMaker<float> {
    type StringMaker<double> (line 2228) | struct StringMaker<double> {
    type StringMaker<T *> (line 2234) | struct StringMaker<T *> {
      method convert (line 2236) | static std::string convert(U *p) {
    type StringMaker<R C::*> (line 2246) | struct StringMaker<R C::*> {
      method convert (line 2247) | static std::string convert(R C::*p) {
    type StringMaker<T ^> (line 2258) | struct StringMaker<T ^> {
      method convert (line 2259) | static std::string convert(T ^ ref) { return ::Catch::Detail::clrRef...
    type Detail (line 2263) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type StringMaker<NSString *> (line 2280) | struct StringMaker<NSString *> {
      method convert (line 2281) | static std::string convert(NSString *nsstring) {
    type StringMaker<NSObject *> (line 2288) | struct StringMaker<NSObject *> {
      method convert (line 2289) | static std::string convert(NSObject *nsObject) {
    type Detail (line 2293) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type StringMaker<std::pair<T1, T2>> (line 2320) | struct StringMaker<std::pair<T1, T2>> {
      method convert (line 2321) | static std::string convert(const std::pair<T1, T2> &pair) {
    type StringMaker<std::optional<T>> (line 2335) | struct StringMaker<std::optional<T>> {
      method convert (line 2336) | static std::string convert(const std::optional<T> &optional) {
    type Detail (line 2353) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type StringMaker<std::monostate> (line 2386) | struct StringMaker<std::monostate> {
      method convert (line 2387) | static std::string convert(const std::monostate &) { return "{ }"; }
    type detail (line 2409) | namespace detail {
      type void_type (line 2411) | struct void_type {
      type is_range_impl (line 2416) | struct is_range_impl : std::false_type {}
      type is_range_impl<T, typename void_type<decltype(begin(std::declval<T>()))>::type> (line 2419) | struct is_range_impl<T, typename void_type<decltype(begin(std::declv...
    type is_range (line 2424) | struct is_range : detail::is_range_impl<T> {}
    type is_range<T ^> (line 2428) | struct is_range<T ^> {
    function rangeToString (line 2434) | std::string rangeToString(Range const &range) {
    function rangeToString (line 2440) | std::string rangeToString(std::vector<bool, Allocator> const &v) {
    type StringMaker<R,
                   typename std::enable_if<is_range<R>::value &&
                                           !::Catch::Detail::IsStreamInsertable<R>::value>::type> (line 2456) | struct StringMaker<R,
      method convert (line 2459) | static std::string convert(R const &range) { return rangeToString(ra...
    type StringMaker<T[SZ]> (line 2463) | struct StringMaker<T[SZ]> {
      method convert (line 2464) | static std::string convert(T const (&arr)[SZ]) { return rangeToStrin...
    type ratio_string (line 2478) | struct ratio_string {
    type ratio_string<std::atto> (line 2489) | struct ratio_string<std::atto> {
    type ratio_string<std::femto> (line 2493) | struct ratio_string<std::femto> {
    type ratio_string<std::pico> (line 2497) | struct ratio_string<std::pico> {
    type ratio_string<std::nano> (line 2501) | struct ratio_string<std::nano> {
    type ratio_string<std::micro> (line 2505) | struct ratio_string<std::micro> {
    type ratio_string<std::milli> (line 2509) | struct ratio_string<std::milli> {
    type StringMaker<std::chrono::duration<Value, Ratio>> (line 2516) | struct StringMaker<std::chrono::duration<Value, Ratio>> {
      method convert (line 2517) | static std::string convert(std::chrono::duration<Value, Ratio> const...
    type StringMaker<std::chrono::duration<Value, std::ratio<1>>> (line 2524) | struct StringMaker<std::chrono::duration<Value, std::ratio<1>>> {
      method convert (line 2525) | static std::string convert(std::chrono::duration<Value, std::ratio<1...
    type StringMaker<std::chrono::duration<Value, std::ratio<60>>> (line 2532) | struct StringMaker<std::chrono::duration<Value, std::ratio<60>>> {
      method convert (line 2533) | static std::string convert(std::chrono::duration<Value, std::ratio<6...
    type StringMaker<std::chrono::duration<Value, std::ratio<3600>>> (line 2540) | struct StringMaker<std::chrono::duration<Value, std::ratio<3600>>> {
      method convert (line 2541) | static std::string convert(std::chrono::duration<Value, std::ratio<3...
    type StringMaker<std::chrono::time_point<Clock, Duration>> (line 2553) | struct StringMaker<std::chrono::time_point<Clock, Duration>> {
      method convert (line 2554) | static std::string convert(std::chrono::time_point<Clock, Duration> ...
    type StringMaker<std::chrono::time_point<std::chrono::system_clock, Duration>> (line 2560) | struct StringMaker<std::chrono::time_point<std::chrono::system_clock, ...
      method convert (line 2561) | static std::string convert(
    type ITransientExpression (line 2621) | struct ITransientExpression {
      method isBinaryExpression (line 2622) | auto isBinaryExpression() const -> bool { return m_isBinaryExpressio...
      method getResult (line 2623) | auto getResult() const -> bool { return m_result; }
      method ITransientExpression (line 2626) | ITransientExpression(bool isBinaryExpression, bool result)
    class BinaryExpr (line 2643) | class BinaryExpr : public ITransientExpression {
      method streamReconstructedExpression (line 2648) | void streamReconstructedExpression(std::ostream &os) const override {
      method BinaryExpr (line 2654) | BinaryExpr(bool comparisonResult, LhsT lhs, StringRef op, RhsT rhs)
    class UnaryExpr (line 2715) | class UnaryExpr : public ITransientExpression {
      method streamReconstructedExpression (line 2718) | void streamReconstructedExpression(std::ostream &os) const override {
      method UnaryExpr (line 2723) | explicit UnaryExpr(LhsT lhs)
    function compareEqual (line 2730) | auto compareEqual(LhsT const &lhs, RhsT const &rhs) -> bool {
    function compareEqual (line 2734) | auto compareEqual(T *const &lhs, int rhs) -> bool {
    function compareEqual (line 2738) | auto compareEqual(T *const &lhs, long rhs) -> bool {
    function compareEqual (line 2742) | auto compareEqual(int lhs, T *const &rhs) -> bool {
    function compareEqual (line 2746) | auto compareEqual(long lhs, T *const &rhs) -> bool {
    function compareNotEqual (line 2751) | auto compareNotEqual(LhsT const &lhs, RhsT &&rhs) -> bool {
    function compareNotEqual (line 2755) | auto compareNotEqual(T *const &lhs, int rhs) -> bool {
    function compareNotEqual (line 2759) | auto compareNotEqual(T *const &lhs, long rhs) -> bool {
    function compareNotEqual (line 2763) | auto compareNotEqual(int lhs, T *const &rhs) -> bool {
    function compareNotEqual (line 2767) | auto compareNotEqual(long lhs, T *const &rhs) -> bool {
    class ExprLhs (line 2772) | class ExprLhs {
      method ExprLhs (line 2776) | explicit ExprLhs(LhsT lhs) : m_lhs(lhs) {}
      method makeUnaryExpr (line 2837) | auto makeUnaryExpr() const -> UnaryExpr<LhsT> { return UnaryExpr<Lhs...
    function handleExpression (line 2843) | void handleExpression(ExprLhs<T> const &expr) {
    type Decomposer (line 2847) | struct Decomposer {
    class AssertionResult (line 2870) | class AssertionResult
      method AssertionResult (line 5808) | AssertionResult() = delete;
    type AssertionInfo (line 2871) | struct AssertionInfo
    type SectionInfo (line 2872) | struct SectionInfo
      method SectionInfo (line 3316) | SectionInfo(SourceLineInfo const &_lineInfo, std::string const &_nam...
    type SectionEndInfo (line 2873) | struct SectionEndInfo
    type MessageInfo (line 2874) | struct MessageInfo
    type MessageBuilder (line 2875) | struct MessageBuilder
      method MessageBuilder (line 3059) | MessageBuilder &operator<<(T const &value) {
    type Counts (line 2876) | struct Counts
    type AssertionReaction (line 2877) | struct AssertionReaction
    type SourceLineInfo (line 2878) | struct SourceLineInfo
      method SourceLineInfo (line 530) | SourceLineInfo() = delete;
      method SourceLineInfo (line 531) | SourceLineInfo(char const *_file, std::size_t _line) noexcept : file...
      method SourceLineInfo (line 533) | SourceLineInfo(SourceLineInfo const &other) = default;
      method SourceLineInfo (line 534) | SourceLineInfo &operator=(SourceLineInfo const &) = default;
      method SourceLineInfo (line 535) | SourceLineInfo(SourceLineInfo &&) noexcept = default;
      method SourceLineInfo (line 536) | SourceLineInfo &operator=(SourceLineInfo &&) noexcept = default;
      method empty (line 538) | bool empty() const noexcept { return file[0] == '\0'; }
    type ITransientExpression (line 2880) | struct ITransientExpression
      method isBinaryExpression (line 2622) | auto isBinaryExpression() const -> bool { return m_isBinaryExpressio...
      method getResult (line 2623) | auto getResult() const -> bool { return m_result; }
      method ITransientExpression (line 2626) | ITransientExpression(bool isBinaryExpression, bool result)
    type IGeneratorTracker (line 2881) | struct IGeneratorTracker
    type BenchmarkInfo (line 2884) | struct BenchmarkInfo
    type BenchmarkStats (line 2886) | struct BenchmarkStats
    type IResultCapture (line 2889) | struct IResultCapture {
    type TestFailureException (line 2945) | struct TestFailureException {}
    type AssertionResultData (line 2946) | struct AssertionResultData
      method AssertionResultData (line 5794) | AssertionResultData() = delete;
    type IResultCapture (line 2947) | struct IResultCapture
    class RunContext (line 2948) | class RunContext
      method RunContext (line 8436) | RunContext(RunContext const &) = delete;
      method RunContext (line 8437) | RunContext &operator=(RunContext const &) = delete;
    class LazyExpression (line 2950) | class LazyExpression {
      method LazyExpression (line 2961) | LazyExpression &operator=(LazyExpression const &) = delete;
    type AssertionReaction (line 2968) | struct AssertionReaction {
    class AssertionHandler (line 2973) | class AssertionHandler {
      method handleExpr (line 2991) | void handleExpr(ExprLhs<T> const &expr) {
    type MessageInfo (line 3025) | struct MessageInfo {
    type MessageStream (line 3043) | struct MessageStream {
      method MessageStream (line 3045) | MessageStream &operator<<(T const &value) {
    type MessageBuilder (line 3053) | struct MessageBuilder : MessageStream {
      method MessageBuilder (line 3059) | MessageBuilder &operator<<(T const &value) {
    class ScopedMessage (line 3067) | class ScopedMessage {
      method ScopedMessage (line 3070) | ScopedMessage(ScopedMessage &duplicate) = delete;
    class Capturer (line 3078) | class Capturer {
      method captureValues (line 3093) | void captureValues(size_t index, T const &value) {
      method captureValues (line 3098) | void captureValues(size_t index, T const &value, Ts const &...values) {
    type Counts (line 3282) | struct Counts {
    type Totals (line 3295) | struct Totals {
    type SectionInfo (line 3312) | struct SectionInfo {
      method SectionInfo (line 3316) | SectionInfo(SourceLineInfo const &_lineInfo, std::string const &_nam...
    type SectionEndInfo (line 3324) | struct SectionEndInfo {
    class Timer (line 3342) | class Timer {
    class Section (line 3360) | class Section : NonCopyable {
    class TestCase (line 3404) | class TestCase
    type ITestCaseRegistry (line 3405) | struct ITestCaseRegistry
    type IExceptionTranslatorRegistry (line 3406) | struct IExceptionTranslatorRegistry
    type IExceptionTranslator (line 3407) | struct IExceptionTranslator
    type IReporterRegistry (line 3408) | struct IReporterRegistry
    type IReporterFactory (line 3409) | struct IReporterFactory
    type ITagAliasRegistry (line 3410) | struct ITagAliasRegistry
    type IMutableEnumValuesRegistry (line 3411) | struct IMutableEnumValuesRegistry
    class StartupExceptionRegistry (line 3413) | class StartupExceptionRegistry
    type IRegistryHub (line 3417) | struct IRegistryHub {
    type IMutableRegistryHub (line 3428) | struct IMutableRegistryHub {
    type IExceptionTranslator (line 3461) | struct IExceptionTranslator
    type IExceptionTranslator (line 3464) | struct IExceptionTranslator {
    type IExceptionTranslatorRegistry (line 3470) | struct IExceptionTranslatorRegistry {
    class ExceptionTranslatorRegistrar (line 3476) | class ExceptionTranslatorRegistrar {
      class ExceptionTranslator (line 3478) | class ExceptionTranslator : public IExceptionTranslator {
        method ExceptionTranslator (line 3480) | ExceptionTranslator(std::string (*translateFunction)(T &))
        method translate (line 3483) | std::string translate(ExceptionTranslators::const_iterator it,
      method ExceptionTranslatorRegistrar (line 3505) | ExceptionTranslatorRegistrar(std::string (*translateFunction)(T &)) {
    type Detail (line 3533) | namespace Detail {
      type EnumInfo (line 1901) | struct EnumInfo {
      function rawMemoryToString (line 1997) | std::string rawMemoryToString(const T &object) {
      class IsStreamInsertable (line 2002) | class IsStreamInsertable {
      function convertUnstreamable (line 2018) | typename std::enable_if<!std::is_enum<T>::value && !std::is_base_of<...
      function convertUnstreamable (line 2024) | typename std::enable_if<!std::is_enum<T>::value && std::is_base_of<s...
      function convertUnstreamable (line 2031) | typename std::enable_if<std::is_enum<T>::value, std::string>::type c...
      function stringify (line 2081) | std::string stringify(const T &e) {
      function convertUnknownEnumToString (line 2087) | std::string convertUnknownEnumToString(E e) {
      function rangeToString (line 2265) | std::string rangeToString(InputIterator first, Sentinel last) {
      function stringify (line 2294) | inline std::string stringify(NSString *nsstring) {
      type TupleElementPrinter (line 2355) | struct TupleElementPrinter {
        method print (line 2356) | static void print(const Tuple &tuple, std::ostream &os) {
      type TupleElementPrinter<Tuple, N, false> (line 2363) | struct TupleElementPrinter<Tuple, N, false> {
        method print (line 2364) | static void print(const Tuple &, std::ostream &) {}
      class Approx (line 3535) | class Approx {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8258) | Approx Approx::custom() { return Approx(0); }
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      function Approx (line 8260) | Approx Approx::operator-() const {
        method Approx (line 3554) | Approx operator()(T const &value) {
        method Approx (line 3564) | explicit Approx(T const &value) : Approx(static_cast<double>(value...
        method Approx (line 3617) | Approx &epsilon(T const &newEpsilon) {
        method Approx (line 3625) | Approx &margin(T const &newMargin) {
        method Approx (line 3633) | Approx &scale(T const &newScale) {
      class EnumValuesRegistry (line 10864) | class EnumValuesRegistry : public IMutableEnumValuesRegistry {
      function StringRef (line 10892) | StringRef extractInstanceName(StringRef enumInstance) {
      function parseEnums (line 10902) | std::vector<StringRef> parseEnums(StringRef enums) {
      function StringRef (line 10914) | StringRef EnumInfo::lookup(int value) const {
      function makeEnumInfo (line 10922) | std::unique_ptr<EnumInfo> makeEnumInfo(StringRef enumName,
      function EnumInfo (line 10938) | EnumInfo const &EnumValuesRegistry::registerEnum(StringRef enumName,
      class StreamBufImpl (line 13821) | class StreamBufImpl : public std::streambuf {
        method StreamBufImpl (line 13826) | StreamBufImpl() { setp(data, data + sizeof(data)); }
        method overflow (line 13831) | int overflow(int c) override {
        method sync (line 13843) | int sync() override {
      type OutputDebugWriter (line 13854) | struct OutputDebugWriter {
      class FileStream (line 13860) | class FileStream : public IStream {
        method FileStream (line 13864) | FileStream(StringRef filename) {
      class CoutStream (line 13876) | class CoutStream : public IStream {
        method CoutStream (line 13882) | CoutStream() : m_os(Catch::cout().rdbuf()) {}
      class DebugOutStream (line 13891) | class DebugOutStream : public IStream {
        method DebugOutStream (line 13896) | DebugOutStream()
      type Endianness (line 15117) | struct Endianness {
        type Arch (line 15118) | enum Arch { Big, Little }
        method Arch (line 15120) | static Arch which() {
      function rawMemoryToString (line 15130) | std::string rawMemoryToString(const void *object, std::size_t size) {
    type literals (line 3648) | namespace literals {
    type StringMaker<Catch::Detail::Approx> (line 3654) | struct StringMaker<Catch::Detail::Approx> {
    type pluralise (line 3687) | struct pluralise {
    type Matchers (line 3707) | namespace Matchers {
      type Impl (line 3708) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3715) | struct MatchNotOf
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
        class MatcherUntypedBase (line 3717) | class MatcherUntypedBase {
          method MatcherUntypedBase (line 3719) | MatcherUntypedBase() = default;
          method MatcherUntypedBase (line 3720) | MatcherUntypedBase(MatcherUntypedBase const &) = default;
          method MatcherUntypedBase (line 3721) | MatcherUntypedBase &operator=(MatcherUntypedBase const &) = delete;
        type MatcherMethod (line 3736) | struct MatcherMethod {
        type MatcherMethod<NSString *> (line 3745) | struct MatcherMethod<NSString *> {
        type MatcherBase (line 3755) | struct MatcherBase : MatcherUntypedBase, MatcherMethod<T> {
        type MatchAllOf (line 3762) | struct MatchAllOf : MatcherBase<ArgT> {
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3795) | struct MatchAnyOf : MatcherBase<ArgT> {
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3829) | struct MatchNotOf : MatcherBase<ArgT> {
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
      type Exception (line 3866) | namespace Exception {
        class ExceptionMessageMatcher (line 3868) | class ExceptionMessageMatcher : public MatcherBase<std::exception> {
          method ExceptionMessageMatcher (line 3872) | ExceptionMessageMatcher(std::string const &message) : m_message(...
      type Floating (line 3892) | namespace Floating {
        type FloatingPointKind (line 3894) | enum class FloatingPointKind : uint8_t
        type WithinAbsMatcher (line 3896) | struct WithinAbsMatcher : MatcherBase<double> {
        type WithinUlpsMatcher (line 3906) | struct WithinUlpsMatcher : MatcherBase<double> {
        type WithinRelMatcher (line 3923) | struct WithinRelMatcher : MatcherBase<double> {
        type FloatingPointKind (line 11833) | enum class FloatingPointKind : uint8_t { Float, Double }
      type Generic (line 3958) | namespace Generic {
        type Detail (line 3960) | namespace Detail {
        class PredicateMatcher (line 3965) | class PredicateMatcher : public MatcherBase<T> {
          method PredicateMatcher (line 3970) | PredicateMatcher(std::function<bool(T const &)> const &elem, std...
          method match (line 3973) | bool match(T const &item) const override { return m_predicate(it...
          method describe (line 3975) | std::string describe() const override { return m_description; }
      function Predicate (line 3985) | Generic::PredicateMatcher<T> Predicate(std::function<bool(T const &)...
      type StdString (line 4001) | namespace StdString {
        type CasedString (line 4003) | struct CasedString {
        type StringMatcherBase (line 4012) | struct StringMatcherBase : MatcherBase<std::string> {
        type EqualsMatcher (line 4020) | struct EqualsMatcher : StringMatcherBase {
        type ContainsMatcher (line 4024) | struct ContainsMatcher : StringMatcherBase {
        type StartsWithMatcher (line 4028) | struct StartsWithMatcher : StringMatcherBase {
        type EndsWithMatcher (line 4032) | struct EndsWithMatcher : StringMatcherBase {
        type RegexMatcher (line 4037) | struct RegexMatcher : MatcherBase<std::string> {
      type Vector (line 4074) | namespace Vector {
        type ContainsElementMatcher (line 4076) | struct ContainsElementMatcher : MatcherBase<std::vector<T, Alloc>> {
          method ContainsElementMatcher (line 4077) | ContainsElementMatcher(T const &comparator) : m_comparator(compa...
          method match (line 4079) | bool match(std::vector<T, Alloc> const &v) const override {
          method describe (line 4088) | std::string describe() const override {
        type ContainsMatcher (line 4096) | struct ContainsMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method ContainsMatcher (line 4097) | ContainsMatcher(std::vector<T, AllocComp> const &comparator) : m...
          method match (line 4099) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4117) | std::string describe() const override {
        type EqualsMatcher (line 4125) | struct EqualsMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method EqualsMatcher (line 4126) | EqualsMatcher(std::vector<T, AllocComp> const &comparator) : m_c...
          method match (line 4128) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4140) | std::string describe() const override {
        type ApproxMatcher (line 4147) | struct ApproxMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method ApproxMatcher (line 4148) | ApproxMatcher(std::vector<T, AllocComp> const &comparator) : m_c...
          method match (line 4150) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4158) | std::string describe() const override {
          method ApproxMatcher (line 4162) | ApproxMatcher &epsilon(T const &newEpsilon) {
          method ApproxMatcher (line 4167) | ApproxMatcher &margin(T const &newMargin) {
          method ApproxMatcher (line 4172) | ApproxMatcher &scale(T const &newScale) {
        type UnorderedEqualsMatcher (line 4182) | struct UnorderedEqualsMatcher : MatcherBase<std::vector<T, AllocMa...
          method UnorderedEqualsMatcher (line 4183) | UnorderedEqualsMatcher(std::vector<T, AllocComp> const &target) ...
          method match (line 4184) | bool match(std::vector<T, AllocMatch> const &vec) const override {
          method describe (line 4191) | std::string describe() const override {
      function Contains (line 4205) | Vector::ContainsMatcher<T, AllocComp, AllocMatch> Contains(
      function VectorContains (line 4211) | Vector::ContainsElementMatcher<T, Alloc> VectorContains(T const &com...
      function Equals (line 4216) | Vector::EqualsMatcher<T, AllocComp, AllocMatch> Equals(
      function Approx (line 4222) | Vector::ApproxMatcher<T, AllocComp, AllocMatch> Approx(
      function UnorderedEquals (line 4228) | Vector::UnorderedEqualsMatcher<T, AllocComp, AllocMatch> UnorderedEq...
      type Impl (line 11679) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3715) | struct MatchNotOf
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
        class MatcherUntypedBase (line 3717) | class MatcherUntypedBase {
          method MatcherUntypedBase (line 3719) | MatcherUntypedBase() = default;
          method MatcherUntypedBase (line 3720) | MatcherUntypedBase(MatcherUntypedBase const &) = default;
          method MatcherUntypedBase (line 3721) | MatcherUntypedBase &operator=(MatcherUntypedBase const &) = delete;
        type MatcherMethod (line 3736) | struct MatcherMethod {
        type MatcherMethod<NSString *> (line 3745) | struct MatcherMethod<NSString *> {
        type MatcherBase (line 3755) | struct MatcherBase : MatcherUntypedBase, MatcherMethod<T> {
        type MatchAllOf (line 3762) | struct MatchAllOf : MatcherBase<ArgT> {
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3795) | struct MatchAnyOf : MatcherBase<ArgT> {
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3829) | struct MatchNotOf : MatcherBase<ArgT> {
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
      type Exception (line 11701) | namespace Exception {
        class ExceptionMessageMatcher (line 3868) | class ExceptionMessageMatcher : public MatcherBase<std::exception> {
          method ExceptionMessageMatcher (line 3872) | ExceptionMessageMatcher(std::string const &message) : m_message(...
      function Message (line 11712) | Exception::ExceptionMessageMatcher Message(std::string const &messag...
      type Floating (line 11831) | namespace Floating {
        type FloatingPointKind (line 3894) | enum class FloatingPointKind : uint8_t
        type WithinAbsMatcher (line 3896) | struct WithinAbsMatcher : MatcherBase<double> {
        type WithinUlpsMatcher (line 3906) | struct WithinUlpsMatcher : MatcherBase<double> {
        type WithinRelMatcher (line 3923) | struct WithinRelMatcher : MatcherBase<double> {
        type FloatingPointKind (line 11833) | enum class FloatingPointKind : uint8_t { Float, Double }
      function WithinULP (line 11928) | Floating::WithinUlpsMatcher WithinULP(double target, uint64_t maxUlp...
      function WithinULP (line 11932) | Floating::WithinUlpsMatcher WithinULP(float target, uint64_t maxUlpD...
      function WithinAbs (line 11936) | Floating::WithinAbsMatcher WithinAbs(double target, double margin) {
      function WithinRel (line 11940) | Floating::WithinRelMatcher WithinRel(double target, double eps) {
      function WithinRel (line 11944) | Floating::WithinRelMatcher WithinRel(double target) {
      function WithinRel (line 11948) | Floating::WithinRelMatcher WithinRel(float target, float eps) {
      function WithinRel (line 11952) | Floating::WithinRelMatcher WithinRel(float target) {
      type StdString (line 11976) | namespace StdString {
        type CasedString (line 4003) | struct CasedString {
        type StringMatcherBase (line 4012) | struct StringMatcherBase : MatcherBase<std::string> {
        type EqualsMatcher (line 4020) | struct EqualsMatcher : StringMatcherBase {
        type ContainsMatcher (line 4024) | struct ContainsMatcher : StringMatcherBase {
        type StartsWithMatcher (line 4028) | struct StartsWithMatcher : StringMatcherBase {
        type EndsWithMatcher (line 4032) | struct EndsWithMatcher : StringMatcherBase {
        type RegexMatcher (line 4037) | struct RegexMatcher : MatcherBase<std::string> {
      function Equals (line 12050) | StdString::EqualsMatcher Equals(std::string const &str, CaseSensitiv...
      function Contains (line 12053) | StdString::ContainsMatcher Contains(std::string const &str, CaseSens...
      function EndsWith (line 12056) | StdString::EndsWithMatcher EndsWith(std::string const &str, CaseSens...
      function StartsWith (line 12059) | StdString::StartsWithMatcher StartsWith(std::string const &str,
      function Matches (line 12064) | StdString::RegexMatcher Matches(std::string const &regex, CaseSensit...
    type Matchers (line 3865) | namespace Matchers {
      type Impl (line 3708) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3715) | struct MatchNotOf
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
        class MatcherUntypedBase (line 3717) | class MatcherUntypedBase {
          method MatcherUntypedBase (line 3719) | MatcherUntypedBase() = default;
          method MatcherUntypedBase (line 3720) | MatcherUntypedBase(MatcherUntypedBase const &) = default;
          method MatcherUntypedBase (line 3721) | MatcherUntypedBase &operator=(MatcherUntypedBase const &) = delete;
        type MatcherMethod (line 3736) | struct MatcherMethod {
        type MatcherMethod<NSString *> (line 3745) | struct MatcherMethod<NSString *> {
        type MatcherBase (line 3755) | struct MatcherBase : MatcherUntypedBase, MatcherMethod<T> {
        type MatchAllOf (line 3762) | struct MatchAllOf : MatcherBase<ArgT> {
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3795) | struct MatchAnyOf : MatcherBase<ArgT> {
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3829) | struct MatchNotOf : MatcherBase<ArgT> {
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
      type Exception (line 3866) | namespace Exception {
        class ExceptionMessageMatcher (line 3868) | class ExceptionMessageMatcher : public MatcherBase<std::exception> {
          method ExceptionMessageMatcher (line 3872) | ExceptionMessageMatcher(std::string const &message) : m_message(...
      type Floating (line 3892) | namespace Floating {
        type FloatingPointKind (line 3894) | enum class FloatingPointKind : uint8_t
        type WithinAbsMatcher (line 3896) | struct WithinAbsMatcher : MatcherBase<double> {
        type WithinUlpsMatcher (line 3906) | struct WithinUlpsMatcher : MatcherBase<double> {
        type WithinRelMatcher (line 3923) | struct WithinRelMatcher : MatcherBase<double> {
        type FloatingPointKind (line 11833) | enum class FloatingPointKind : uint8_t { Float, Double }
      type Generic (line 3958) | namespace Generic {
        type Detail (line 3960) | namespace Detail {
        class PredicateMatcher (line 3965) | class PredicateMatcher : public MatcherBase<T> {
          method PredicateMatcher (line 3970) | PredicateMatcher(std::function<bool(T const &)> const &elem, std...
          method match (line 3973) | bool match(T const &item) const override { return m_predicate(it...
          method describe (line 3975) | std::string describe() const override { return m_description; }
      function Predicate (line 3985) | Generic::PredicateMatcher<T> Predicate(std::function<bool(T const &)...
      type StdString (line 4001) | namespace StdString {
        type CasedString (line 4003) | struct CasedString {
        type StringMatcherBase (line 4012) | struct StringMatcherBase : MatcherBase<std::string> {
        type EqualsMatcher (line 4020) | struct EqualsMatcher : StringMatcherBase {
        type ContainsMatcher (line 4024) | struct ContainsMatcher : StringMatcherBase {
        type StartsWithMatcher (line 4028) | struct StartsWithMatcher : StringMatcherBase {
        type EndsWithMatcher (line 4032) | struct EndsWithMatcher : StringMatcherBase {
        type RegexMatcher (line 4037) | struct RegexMatcher : MatcherBase<std::string> {
      type Vector (line 4074) | namespace Vector {
        type ContainsElementMatcher (line 4076) | struct ContainsElementMatcher : MatcherBase<std::vector<T, Alloc>> {
          method ContainsElementMatcher (line 4077) | ContainsElementMatcher(T const &comparator) : m_comparator(compa...
          method match (line 4079) | bool match(std::vector<T, Alloc> const &v) const override {
          method describe (line 4088) | std::string describe() const override {
        type ContainsMatcher (line 4096) | struct ContainsMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method ContainsMatcher (line 4097) | ContainsMatcher(std::vector<T, AllocComp> const &comparator) : m...
          method match (line 4099) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4117) | std::string describe() const override {
        type EqualsMatcher (line 4125) | struct EqualsMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method EqualsMatcher (line 4126) | EqualsMatcher(std::vector<T, AllocComp> const &comparator) : m_c...
          method match (line 4128) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4140) | std::string describe() const override {
        type ApproxMatcher (line 4147) | struct ApproxMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method ApproxMatcher (line 4148) | ApproxMatcher(std::vector<T, AllocComp> const &comparator) : m_c...
          method match (line 4150) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4158) | std::string describe() const override {
          method ApproxMatcher (line 4162) | ApproxMatcher &epsilon(T const &newEpsilon) {
          method ApproxMatcher (line 4167) | ApproxMatcher &margin(T const &newMargin) {
          method ApproxMatcher (line 4172) | ApproxMatcher &scale(T const &newScale) {
        type UnorderedEqualsMatcher (line 4182) | struct UnorderedEqualsMatcher : MatcherBase<std::vector<T, AllocMa...
          method UnorderedEqualsMatcher (line 4183) | UnorderedEqualsMatcher(std::vector<T, AllocComp> const &target) ...
          method match (line 4184) | bool match(std::vector<T, AllocMatch> const &vec) const override {
          method describe (line 4191) | std::string describe() const override {
      function Contains (line 4205) | Vector::ContainsMatcher<T, AllocComp, AllocMatch> Contains(
      function VectorContains (line 4211) | Vector::ContainsElementMatcher<T, Alloc> VectorContains(T const &com...
      function Equals (line 4216) | Vector::EqualsMatcher<T, AllocComp, AllocMatch> Equals(
      function Approx (line 4222) | Vector::ApproxMatcher<T, AllocComp, AllocMatch> Approx(
      function UnorderedEquals (line 4228) | Vector::UnorderedEqualsMatcher<T, AllocComp, AllocMatch> UnorderedEq...
      type Impl (line 11679) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3715) | struct MatchNotOf
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
        class MatcherUntypedBase (line 3717) | class MatcherUntypedBase {
          method MatcherUntypedBase (line 3719) | MatcherUntypedBase() = default;
          method MatcherUntypedBase (line 3720) | MatcherUntypedBase(MatcherUntypedBase const &) = default;
          method MatcherUntypedBase (line 3721) | MatcherUntypedBase &operator=(MatcherUntypedBase const &) = delete;
        type MatcherMethod (line 3736) | struct MatcherMethod {
        type MatcherMethod<NSString *> (line 3745) | struct MatcherMethod<NSString *> {
        type MatcherBase (line 3755) | struct MatcherBase : MatcherUntypedBase, MatcherMethod<T> {
        type MatchAllOf (line 3762) | struct MatchAllOf : MatcherBase<ArgT> {
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3795) | struct MatchAnyOf : MatcherBase<ArgT> {
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3829) | struct MatchNotOf : MatcherBase<ArgT> {
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
      type Exception (line 11701) | namespace Exception {
        class ExceptionMessageMatcher (line 3868) | class ExceptionMessageMatcher : public MatcherBase<std::exception> {
          method ExceptionMessageMatcher (line 3872) | ExceptionMessageMatcher(std::string const &message) : m_message(...
      function Message (line 11712) | Exception::ExceptionMessageMatcher Message(std::string const &messag...
      type Floating (line 11831) | namespace Floating {
        type FloatingPointKind (line 3894) | enum class FloatingPointKind : uint8_t
        type WithinAbsMatcher (line 3896) | struct WithinAbsMatcher : MatcherBase<double> {
        type WithinUlpsMatcher (line 3906) | struct WithinUlpsMatcher : MatcherBase<double> {
        type WithinRelMatcher (line 3923) | struct WithinRelMatcher : MatcherBase<double> {
        type FloatingPointKind (line 11833) | enum class FloatingPointKind : uint8_t { Float, Double }
      function WithinULP (line 11928) | Floating::WithinUlpsMatcher WithinULP(double target, uint64_t maxUlp...
      function WithinULP (line 11932) | Floating::WithinUlpsMatcher WithinULP(float target, uint64_t maxUlpD...
      function WithinAbs (line 11936) | Floating::WithinAbsMatcher WithinAbs(double target, double margin) {
      function WithinRel (line 11940) | Floating::WithinRelMatcher WithinRel(double target, double eps) {
      function WithinRel (line 11944) | Floating::WithinRelMatcher WithinRel(double target) {
      function WithinRel (line 11948) | Floating::WithinRelMatcher WithinRel(float target, float eps) {
      function WithinRel (line 11952) | Floating::WithinRelMatcher WithinRel(float target) {
      type StdString (line 11976) | namespace StdString {
        type CasedString (line 4003) | struct CasedString {
        type StringMatcherBase (line 4012) | struct StringMatcherBase : MatcherBase<std::string> {
        type EqualsMatcher (line 4020) | struct EqualsMatcher : StringMatcherBase {
        type ContainsMatcher (line 4024) | struct ContainsMatcher : StringMatcherBase {
        type StartsWithMatcher (line 4028) | struct StartsWithMatcher : StringMatcherBase {
        type EndsWithMatcher (line 4032) | struct EndsWithMatcher : StringMatcherBase {
        type RegexMatcher (line 4037) | struct RegexMatcher : MatcherBase<std::string> {
      function Equals (line 12050) | StdString::EqualsMatcher Equals(std::string const &str, CaseSensitiv...
      function Contains (line 12053) | StdString::ContainsMatcher Contains(std::string const &str, CaseSens...
      function EndsWith (line 12056) | StdString::EndsWithMatcher EndsWith(std::string const &str, CaseSens...
      function StartsWith (line 12059) | StdString::StartsWithMatcher StartsWith(std::string const &str,
      function Matches (line 12064) | StdString::RegexMatcher Matches(std::string const &regex, CaseSensit...
    type Matchers (line 3890) | namespace Matchers {
      type Impl (line 3708) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3715) | struct MatchNotOf
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
        class MatcherUntypedBase (line 3717) | class MatcherUntypedBase {
          method MatcherUntypedBase (line 3719) | MatcherUntypedBase() = default;
          method MatcherUntypedBase (line 3720) | MatcherUntypedBase(MatcherUntypedBase const &) = default;
          method MatcherUntypedBase (line 3721) | MatcherUntypedBase &operator=(MatcherUntypedBase const &) = delete;
        type MatcherMethod (line 3736) | struct MatcherMethod {
        type MatcherMethod<NSString *> (line 3745) | struct MatcherMethod<NSString *> {
        type MatcherBase (line 3755) | struct MatcherBase : MatcherUntypedBase, MatcherMethod<T> {
        type MatchAllOf (line 3762) | struct MatchAllOf : MatcherBase<ArgT> {
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3795) | struct MatchAnyOf : MatcherBase<ArgT> {
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3829) | struct MatchNotOf : MatcherBase<ArgT> {
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
      type Exception (line 3866) | namespace Exception {
        class ExceptionMessageMatcher (line 3868) | class ExceptionMessageMatcher : public MatcherBase<std::exception> {
          method ExceptionMessageMatcher (line 3872) | ExceptionMessageMatcher(std::string const &message) : m_message(...
      type Floating (line 3892) | namespace Floating {
        type FloatingPointKind (line 3894) | enum class FloatingPointKind : uint8_t
        type WithinAbsMatcher (line 3896) | struct WithinAbsMatcher : MatcherBase<double> {
        type WithinUlpsMatcher (line 3906) | struct WithinUlpsMatcher : MatcherBase<double> {
        type WithinRelMatcher (line 3923) | struct WithinRelMatcher : MatcherBase<double> {
        type FloatingPointKind (line 11833) | enum class FloatingPointKind : uint8_t { Float, Double }
      type Generic (line 3958) | namespace Generic {
        type Detail (line 3960) | namespace Detail {
        class PredicateMatcher (line 3965) | class PredicateMatcher : public MatcherBase<T> {
          method PredicateMatcher (line 3970) | PredicateMatcher(std::function<bool(T const &)> const &elem, std...
          method match (line 3973) | bool match(T const &item) const override { return m_predicate(it...
          method describe (line 3975) | std::string describe() const override { return m_description; }
      function Predicate (line 3985) | Generic::PredicateMatcher<T> Predicate(std::function<bool(T const &)...
      type StdString (line 4001) | namespace StdString {
        type CasedString (line 4003) | struct CasedString {
        type StringMatcherBase (line 4012) | struct StringMatcherBase : MatcherBase<std::string> {
        type EqualsMatcher (line 4020) | struct EqualsMatcher : StringMatcherBase {
        type ContainsMatcher (line 4024) | struct ContainsMatcher : StringMatcherBase {
        type StartsWithMatcher (line 4028) | struct StartsWithMatcher : StringMatcherBase {
        type EndsWithMatcher (line 4032) | struct EndsWithMatcher : StringMatcherBase {
        type RegexMatcher (line 4037) | struct RegexMatcher : MatcherBase<std::string> {
      type Vector (line 4074) | namespace Vector {
        type ContainsElementMatcher (line 4076) | struct ContainsElementMatcher : MatcherBase<std::vector<T, Alloc>> {
          method ContainsElementMatcher (line 4077) | ContainsElementMatcher(T const &comparator) : m_comparator(compa...
          method match (line 4079) | bool match(std::vector<T, Alloc> const &v) const override {
          method describe (line 4088) | std::string describe() const override {
        type ContainsMatcher (line 4096) | struct ContainsMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method ContainsMatcher (line 4097) | ContainsMatcher(std::vector<T, AllocComp> const &comparator) : m...
          method match (line 4099) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4117) | std::string describe() const override {
        type EqualsMatcher (line 4125) | struct EqualsMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method EqualsMatcher (line 4126) | EqualsMatcher(std::vector<T, AllocComp> const &comparator) : m_c...
          method match (line 4128) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4140) | std::string describe() const override {
        type ApproxMatcher (line 4147) | struct ApproxMatcher : MatcherBase<std::vector<T, AllocMatch>> {
          method ApproxMatcher (line 4148) | ApproxMatcher(std::vector<T, AllocComp> const &comparator) : m_c...
          method match (line 4150) | bool match(std::vector<T, AllocMatch> const &v) const override {
          method describe (line 4158) | std::string describe() const override {
          method ApproxMatcher (line 4162) | ApproxMatcher &epsilon(T const &newEpsilon) {
          method ApproxMatcher (line 4167) | ApproxMatcher &margin(T const &newMargin) {
          method ApproxMatcher (line 4172) | ApproxMatcher &scale(T const &newScale) {
        type UnorderedEqualsMatcher (line 4182) | struct UnorderedEqualsMatcher : MatcherBase<std::vector<T, AllocMa...
          method UnorderedEqualsMatcher (line 4183) | UnorderedEqualsMatcher(std::vector<T, AllocComp> const &target) ...
          method match (line 4184) | bool match(std::vector<T, AllocMatch> const &vec) const override {
          method describe (line 4191) | std::string describe() const override {
      function Contains (line 4205) | Vector::ContainsMatcher<T, AllocComp, AllocMatch> Contains(
      function VectorContains (line 4211) | Vector::ContainsElementMatcher<T, Alloc> VectorContains(T const &com...
      function Equals (line 4216) | Vector::EqualsMatcher<T, AllocComp, AllocMatch> Equals(
      function Approx (line 4222) | Vector::ApproxMatcher<T, AllocComp, AllocMatch> Approx(
      function UnorderedEquals (line 4228) | Vector::UnorderedEqualsMatcher<T, AllocComp, AllocMatch> UnorderedEq...
      type Impl (line 11679) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3715) | struct MatchNotOf
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
        class MatcherUntypedBase (line 3717) | class MatcherUntypedBase {
          method MatcherUntypedBase (line 3719) | MatcherUntypedBase() = default;
          method MatcherUntypedBase (line 3720) | MatcherUntypedBase(MatcherUntypedBase const &) = default;
          method MatcherUntypedBase (line 3721) | MatcherUntypedBase &operator=(MatcherUntypedBase const &) = delete;
        type MatcherMethod (line 3736) | struct MatcherMethod {
        type MatcherMethod<NSString *> (line 3745) | struct MatcherMethod<NSString *> {
        type MatcherBase (line 3755) | struct MatcherBase : MatcherUntypedBase, MatcherMethod<T> {
        type MatchAllOf (line 3762) | struct MatchAllOf : MatcherBase<ArgT> {
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3795) | struct MatchAnyOf : MatcherBase<ArgT> {
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | std::string describe() const override {
        type MatchNotOf (line 3829) | struct MatchNotOf : MatcherBase<ArgT> {
          method MatchNotOf (line 3830) | MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
          method match (line 3833) | bool match(ArgT const &arg) const override { return !m_underlyin...
          method describe (line 3835) | std::string describe() const override { return "not " + m_underl...
      type Exception (line 11701) | namespace Exception {
        class ExceptionMessageMatcher (line 3868) | class ExceptionMessageMatcher : public MatcherBase<std::exception> {
          method ExceptionMessageMatcher (line 3872) | ExceptionMessageMatcher(std::string const &message) : m_message(...
      function Message (line 11712) | Exception::ExceptionMessageMatcher Message(std::string const &messag...
      type Floating (line 11831) | namespace Floating {
        type FloatingPointKind (line 3894) | enum class FloatingPointKind : uint8_t
        type WithinAbsMatcher (line 3896) | struct WithinAbsMatcher : MatcherBase<double> {
        type WithinUlpsMatcher (line 3906) | struct WithinUlpsMatcher : MatcherBase<double> {
        type WithinRelMatcher (line 3923) | struct WithinRelMatcher : MatcherBase<double> {
        type FloatingPointKind (line 11833) | enum class FloatingPointKind : uint8_t { Float, Double }
      function WithinULP (line 11928) | Floating::WithinUlpsMatcher WithinULP(double target, uint64_t maxUlp...
      function WithinULP (line 11932) | Floating::WithinUlpsMatcher WithinULP(float target, uint64_t maxUlpD...
      function WithinAbs (line 11936) | Floating::WithinAbsMatcher WithinAbs(double target, double margin) {
      function WithinRel (line 11940) | Floating::WithinRelMatcher WithinRel(double target, double eps) {
      function WithinRel (line 11944) | Floating::WithinRelMatcher WithinRel(double target) {
      function WithinRel (line 11948) | Floating::WithinRelMatcher WithinRel(float target, float eps) {
      function WithinRel (line 11952) | Floating::WithinRelMatcher WithinRel(float target) {
      type StdString (line 11976) | namespace StdString {
        type CasedString (line 4003) | struct CasedString {
        type StringMatcherBase (line 4012) | struct StringMatcherBase : MatcherBase<std::string> {
        type EqualsMatcher (line 4020) | struct EqualsMatcher : StringMatcherBase {
        type ContainsMatcher (line 4024) | struct ContainsMatcher : StringMatcherBase {
        type StartsWithMatcher (line 4028) | struct StartsWithMatcher : StringMatcherBase {
        type EndsWithMatcher (line 4032) | struct EndsWithMatcher : StringMatcherBase {
        type RegexMatcher (line 4037) | struct RegexMatcher : MatcherBase<std::string> {
      function Equals (line 12050) | StdString::EqualsMatcher Equals(std::string const &str, CaseSensitiv...
      function Contains (line 12053) | StdString::ContainsMatcher Contains(std::string const &str, CaseSens...
      function EndsWith (line 12056) | StdString::EndsWithMatcher EndsWith(std::string const &str, CaseSens...
      function StartsWith (line 12059) | StdString::StartsWithMatcher StartsWith(std::string const &str,
      function Matches (line 12064) | StdString::RegexMatcher Matches(std::string const &regex, CaseSensit...
    type Matchers (line 3957) | namespace Matchers {
      type Impl (line 3708) | namespace Impl {
        type MatchAllOf (line 3711) | struct MatchAllOf
          method match (line 3763) | bool match(ArgT const &arg) const override {
          method describe (line 3770) | std::string describe() const override {
        type MatchAnyOf (line 3713) | struct MatchAnyOf
          method match (line 3796) | bool match(ArgT const &arg) const override {
          method describe (line 3803) | st

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  {
    "path": ".codespellrc",
    "chars": 834,
    "preview": "# Waiting for pyproject.toml support: https://github.com/codespell-project/codespell/issues/2055\n\n[codespell]\n# \"write-c"
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  {
    "path": ".flake8",
    "chars": 196,
    "preview": "# Waiting for pyproject.toml support: https://gitlab.com/pycqa/flake8/-/issues/428\n\n[flake8]\nextend-ignore = E203, W503\n"
  },
  {
    "path": ".gitattributes",
    "chars": 1975,
    "preview": "# Based on https://github.com/alexkaratarakis/gitattributes\n# Auto detect text files and force linux-style line endings\n"
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  {
    "path": ".github/ISSUE_TEMPLATE/bug_report.md",
    "chars": 443,
    "preview": "---\nname: Bug report\nabout: Create a report to help us improve\ntitle: ''\nlabels: ''\nassignees: ''\n\n---\n\n## Issue Descrip"
  },
  {
    "path": ".gitignore",
    "chars": 302,
    "preview": "build*/\n.conan/\ncmake-build*/\nCMakeUserPresets.json\n_build/\n.conan/\n.cache/\ndist/\n.DS_Store\n.pod5\nvenv/\n*.venv/\nuv.lock\n"
  },
  {
    "path": ".gitlab-ci.yml",
    "chars": 35332,
    "preview": "stages:\n  - .pre\n  - build\n  - test\n  - build-conan\n  - archive\n  - deploy\n\ninclude:\n    - local: '/ci/gitlab-ci-common."
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  {
    "path": ".gitmodules",
    "chars": 127,
    "preview": "[submodule \"third_party/pybind11\"]\n\tpath = third_party/pybind11\n\turl = https://github.com/pybind/pybind11.git\n\tbranch = "
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  {
    "path": ".pre-commit-config.yaml",
    "chars": 1623,
    "preview": "# See https://pre-commit.com for more information\n# See https://pre-commit.com/hooks.html for more hooks\nrepos:\n  - repo"
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  {
    "path": ".readthedocs.yaml",
    "chars": 709,
    "preview": "# Read the Docs configuration file\n# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details\n\n# Requir"
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  {
    "path": "CHANGELOG.md",
    "chars": 21363,
    "preview": "<!-- markdownlint-disable MD024 -->\n\n# Changelog\n\nAll notable changes, updates, and fixes to pod5 will be documented her"
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    "path": "CMakeLists.txt",
    "chars": 5267,
    "preview": "cmake_minimum_required(VERSION 3.18.0)\n\nproject(POD5)\n\ninclude(${PROJECT_SOURCE_DIR}/cmake/POD5Version.cmake)\n\nset(CMAKE"
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  {
    "path": "CMakePresets.json",
    "chars": 14197,
    "preview": "{\n    \"version\": 4,\n    \"include\": [\n        \"cmake/presets/conan-provider.json\",\n        \"cmake/presets/conan-build-opt"
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  {
    "path": "DEV.md",
    "chars": 1762,
    "preview": "Development\n===========\n\nIf you want to contribute to pod5_file_format, or our pre-built binaries do not meet your platf"
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  {
    "path": "LICENSE.md",
    "chars": 15712,
    "preview": "This Source Code Form is subject to the terms of the Mozilla Public\nLicense, v. 2.0. If a copy of the MPL was not distri"
  },
  {
    "path": "README.md",
    "chars": 1556,
    "preview": "[![Documentation Status](https://readthedocs.org/projects/pod5-file-format/badge/?version=latest)](https://pod5-file-for"
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  {
    "path": "benchmarks/.gitignore",
    "chars": 23,
    "preview": "*/outputs/\nimage/*.whl\n"
  },
  {
    "path": "benchmarks/README.md",
    "chars": 2529,
    "preview": "POD5 Benchmarks\n==============\n\nBuilding the benchmark environment\n----------------------------------\n\nTo run benchmarks"
  },
  {
    "path": "benchmarks/build.sh",
    "chars": 243,
    "preview": "#!/bin/bash\n\nset -o errexit\nset -o pipefail\nset -o nounset\n# set -o xtrace\n\nscript_dir=$( cd -- \"$( dirname -- \"${BASH_S"
  },
  {
    "path": "benchmarks/convert/run_blow5.sh",
    "chars": 101,
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  {
    "path": "benchmarks/convert/run_pod5.sh",
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  {
    "path": "benchmarks/find_all_read_ids/run_blow5.sh",
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    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\n\ntools/pyslow5_tests.py \"${input_dir}\"/blow5/*.blow5 \"${output_dir}\" get_all_rea"
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  {
    "path": "benchmarks/find_all_read_ids/run_pod5.sh",
    "chars": 106,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\n\n./tools/find_and_get_pod5.py \"${input_dir}/pod5\" \"${output_dir}\"\n"
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  {
    "path": "benchmarks/find_all_samples/run_blow5.sh",
    "chars": 141,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\n\ntools/pyslow5_tests.py \"${input_dir}\"/blow5/*.blow5 \"${output_dir}\" all_values "
  },
  {
    "path": "benchmarks/find_all_samples/run_fast5.sh",
    "chars": 127,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\n\ntools/find_and_get_fast5.py \"${input_dir}/fast5\" \"${output_dir}\" --get-column s"
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  {
    "path": "benchmarks/find_all_samples/run_pod5.sh",
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    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\n\n./tools/find_and_get_pod5.py \"${input_dir}/pod5\" \"${output_dir}\" --get-column s"
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    "path": "benchmarks/find_selected_read_ids_read_number/run_blow5.sh",
    "chars": 223,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\nfull_output_dir=$3\n\ntools/pyslow5_tests.py \"${input_dir}\"/blow5/*.blow5 \"${outpu"
  },
  {
    "path": "benchmarks/find_selected_read_ids_read_number/run_fast5.sh",
    "chars": 206,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\nfull_output_dir=$3\n\ntools/find_and_get_fast5.py \"${input_dir}/fast5\" \"${output_d"
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  {
    "path": "benchmarks/find_selected_read_ids_read_number/run_pod5.sh",
    "chars": 216,
    "preview": "#!/bin/bash\n\ninput_dir=$1\ntype_output_dir=$2\nfull_output_dir=$3\n\n./tools/find_and_get_pod5.py \"${input_dir}/pod5\" \"${typ"
  },
  {
    "path": "benchmarks/find_selected_read_ids_sample_count/run_blow5.sh",
    "chars": 224,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\nfull_output_dir=$3\n\ntools/pyslow5_tests.py \"${input_dir}\"/blow5/*.blow5 \"${outpu"
  },
  {
    "path": "benchmarks/find_selected_read_ids_sample_count/run_fast5.sh",
    "chars": 207,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\nfull_output_dir=$3\n\ntools/find_and_get_fast5.py \"${input_dir}/fast5\" \"${output_d"
  },
  {
    "path": "benchmarks/find_selected_read_ids_sample_count/run_pod5.sh",
    "chars": 217,
    "preview": "#!/bin/bash\n\ninput_dir=$1\ntype_output_dir=$2\nfull_output_dir=$3\n\n./tools/find_and_get_pod5.py \"${input_dir}/pod5\" \"${typ"
  },
  {
    "path": "benchmarks/find_selected_read_ids_samples/run_blow5.sh",
    "chars": 219,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\nfull_output_dir=$3\n\ntools/pyslow5_tests.py \"${input_dir}\"/blow5/*.blow5 \"${outpu"
  },
  {
    "path": "benchmarks/find_selected_read_ids_samples/run_fast5.sh",
    "chars": 202,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\nfull_output_dir=$3\n\ntools/find_and_get_fast5.py \"${input_dir}/fast5\" \"${output_d"
  },
  {
    "path": "benchmarks/find_selected_read_ids_samples/run_pod5.sh",
    "chars": 212,
    "preview": "#!/bin/bash\n\ninput_dir=$1\ntype_output_dir=$2\nfull_output_dir=$3\n\n./tools/find_and_get_pod5.py \"${input_dir}/pod5\" \"${typ"
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    "path": "benchmarks/image/Dockerfile.base",
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    "preview": "FROM ubuntu:20.04\n\nRUN apt update && apt install -y wget python3 python3-pip git libzstd-dev\n\nRUN wget https://github.co"
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    "path": "benchmarks/image/install_slow5.sh",
    "chars": 996,
    "preview": "#!/bin/bash\n\nset -e\n\n: \"${SLOW_5_TOOLS_VERSION:=v1.3.0}\"\n: \"${SLOW_5_LIB_VERSION:=v1.3.1}\"\n\napt update\napt install -y li"
  },
  {
    "path": "benchmarks/image/requirements-benchmarks.txt",
    "chars": 27,
    "preview": "h5py\nnumpy\npandas\ntabulate\n"
  },
  {
    "path": "benchmarks/run_benchmarks.py",
    "chars": 8334,
    "preview": "#!/usr/bin/env python3\n\"\"\"\nExample usage:\n```\n> taskset -c 0-10 ./benchmarks/run_benchmarks.py ./input_files/ \\\n    ./be"
  },
  {
    "path": "benchmarks/run_benchmarks_in_docker.sh",
    "chars": 422,
    "preview": "#!/bin/bash\n\nset -e\n\ninput_dir=$(readlink -f \"$1\")\noutput_dir=\"$(pwd)/pod5-benchmark-outputs\"\nmkdir -p \"${output_dir}\"\n\n"
  },
  {
    "path": "benchmarks/tools/check_csvs_consistent.py",
    "chars": 724,
    "preview": "#!/usr/bin/env python3\n\nimport argparse\nimport sys\n\nimport pandas as pd\nfrom pandas.testing import assert_frame_equal\n\n\n"
  },
  {
    "path": "benchmarks/tools/fast5_to_single_blow5.sh",
    "chars": 1465,
    "preview": "#!/bin/bash\n\ninput_path=$1\noutput_path=$2\n\nmkdir -p \"$output_path\"\n\ntemp_dir=\"${output_path}/tmp\"\nmkdir -p \"$temp_dir\"\n\n"
  },
  {
    "path": "benchmarks/tools/find_and_get_fast5.py",
    "chars": 2550,
    "preview": "#!/usr/bin/env python3\n\nimport argparse\nfrom pathlib import Path\n\nimport h5py\nimport numpy\nimport pandas as pd\n\n\ndef sel"
  },
  {
    "path": "benchmarks/tools/find_and_get_pod5.py",
    "chars": 8611,
    "preview": "#!/usr/bin/env python3\n\nimport argparse\nimport multiprocessing as mp\nimport tempfile\nfrom collections import namedtuple\n"
  },
  {
    "path": "benchmarks/tools/pyslow5_tests.py",
    "chars": 4672,
    "preview": "#!/usr/bin/env python3\n\nimport argparse\nimport multiprocessing as mp\nfrom pathlib import Path\nfrom queue import Empty\n\ni"
  },
  {
    "path": "benchmarks/tools/run_benchmarks_docker_entry.sh",
    "chars": 171,
    "preview": "#!/bin/bash\n\n# Use taskset to limit benchmarks to specific cores, ensuring a fair test of limited resources:\ntaskset -c "
  },
  {
    "path": "benchmarks/tools/select-random-ids.py",
    "chars": 566,
    "preview": "#!/usr/bin/env python3\n\nimport argparse\nfrom pathlib import Path\n\nimport pandas as pd\n\n\ndef main():\n    parser = argpars"
  },
  {
    "path": "c++/CMakeLists.txt",
    "chars": 7025,
    "preview": "\n\nif (ENABLE_CONAN)\n    find_package(Arrow REQUIRED CONFIG)\n    find_package(Flatbuffers REQUIRED CONFIG)\n    find_packa"
  },
  {
    "path": "c++/examples/CMakeLists.txt",
    "chars": 1007,
    "preview": "add_executable(find_all_read_ids\n    find_all_read_ids.cpp\n)\n\ntarget_link_libraries(find_all_read_ids\n    pod5_format\n)\n"
  },
  {
    "path": "c++/examples/README.md",
    "chars": 365,
    "preview": "C++ Examples\n============\n\nThese examples use the POD5 C API to read file data, they are written using C++.\n\nfind_all_re"
  },
  {
    "path": "c++/examples/find_all_read_data.cpp",
    "chars": 3317,
    "preview": "#include \"pod5_format/c_api.h\"\n#include \"pod5_format/uuid.h\"\n\n#include <array>\n#include <fstream>\n#include <iostream>\n#i"
  },
  {
    "path": "c++/examples/find_all_read_ids.cpp",
    "chars": 3075,
    "preview": "#include \"pod5_format/c_api.h\"\n#include \"pod5_format/uuid.h\"\n\n#include <array>\n#include <fstream>\n#include <iostream>\n#i"
  },
  {
    "path": "c++/examples/find_specific_read_ids.cpp",
    "chars": 4526,
    "preview": "#include \"pod5_format/c_api.h\"\n#include \"pod5_format/uuid.h\"\n\n#include <fstream>\n#include <iostream>\n#include <vector>\n\n"
  },
  {
    "path": "c++/examples/find_specific_read_ids_with_signal.cpp",
    "chars": 5223,
    "preview": "#include \"pod5_format/c_api.h\"\n#include \"pod5_format/uuid.h\"\n\n#include <fstream>\n#include <iostream>\n#include <vector>\n\n"
  },
  {
    "path": "c++/pod5_format/async_signal_loader.cpp",
    "chars": 8821,
    "preview": "#include \"pod5_format/async_signal_loader.h\"\n\nnamespace pod5 {\n\nstd::size_t const AsyncSignalLoader::MINIMUM_JOB_SIZE = "
  },
  {
    "path": "c++/pod5_format/async_signal_loader.h",
    "chars": 6490,
    "preview": "#pragma once\n\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/rea"
  },
  {
    "path": "c++/pod5_format/c_api.cpp",
    "chars": 49564,
    "preview": "#include \"pod5_format/c_api.h\"\n\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format/file_writer.h\"\n#include \"pod5"
  },
  {
    "path": "c++/pod5_format/c_api.h",
    "chars": 40532,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n\n#include <stddef.h>\n#include <stdint.h>\n\n#ifdef __cplusplus\ne"
  },
  {
    "path": "c++/pod5_format/dictionary_writer.h",
    "chars": 584,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n\nnamespace arrow {\nclass Array"
  },
  {
    "path": "c++/pod5_format/expandable_buffer.h",
    "chars": 3952,
    "preview": "#pragma once\n\n#include <arrow/buffer.h>\n#include <arrow/result.h>\n#include <gsl/gsl-lite.hpp>\n\n#include <cassert>\n\nnames"
  },
  {
    "path": "c++/pod5_format/file_output_stream.h",
    "chars": 312,
    "preview": "#pragma once\n\n#include <arrow/io/file.h>\n#include <arrow/status.h>\n\nnamespace pod5 {\n\nclass FileOutputStream : public ar"
  },
  {
    "path": "c++/pod5_format/file_reader.cpp",
    "chars": 10853,
    "preview": "#include \"pod5_format/file_reader.h\"\n\n#include \"pod5_format/internal/combined_file_utils.h\"\n#include \"pod5_format/memory"
  },
  {
    "path": "c++/pod5_format/file_reader.h",
    "chars": 4590,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/read_table_utils.h\"\n#include \"pod5_forma"
  },
  {
    "path": "c++/pod5_format/file_recovery.h",
    "chars": 2398,
    "preview": "#pragma once\n\n#include \"pod5_format/internal/combined_file_utils.h\"\n#include \"pod5_format/schema_metadata.h\"\n\n#include <"
  },
  {
    "path": "c++/pod5_format/file_updater.cpp",
    "chars": 2088,
    "preview": "#include \"pod5_format/file_updater.h\"\n\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format/internal/combined_file"
  },
  {
    "path": "c++/pod5_format/file_updater.h",
    "chars": 585,
    "preview": "#pragma once\n\n#include \"pod5_format/result.h\"\n\n#include <memory>\n\nnamespace arrow {\nclass MemoryPool;\n}\n\nnamespace pod5 "
  },
  {
    "path": "c++/pod5_format/file_writer.cpp",
    "chars": 30303,
    "preview": "#include \"pod5_format/file_writer.h\"\n\n#include \"pod5_format/file_recovery.h\"\n#include \"pod5_format/internal/async_output"
  },
  {
    "path": "c++/pod5_format/file_writer.h",
    "chars": 7503,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/read_table_utils.h\"\n#include \"pod5_forma"
  },
  {
    "path": "c++/pod5_format/flatbuffers/footer.fbs",
    "chars": 1409,
    "preview": "namespace Minknow.ReadsFormat;\n\nenum ContentType:short {\n    // The Reads table (an Arrow table)\n    ReadsTable,\n    // "
  },
  {
    "path": "c++/pod5_format/internal/async_output_stream.h",
    "chars": 7915,
    "preview": "#pragma once\n\n#include \"pod5_format/file_output_stream.h\"\n#include \"pod5_format/internal/tracing/tracing.h\"\n#include \"po"
  },
  {
    "path": "c++/pod5_format/internal/combined_file_utils.h",
    "chars": 16507,
    "preview": "#pragma once\n\n#include \"pod5_flatbuffers/footer_generated.h\"\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format/"
  },
  {
    "path": "c++/pod5_format/internal/linux_output_stream.h",
    "chars": 14404,
    "preview": "#pragma once\n\n#include \"pod5_format/file_output_stream.h\"\n#include \"pod5_format/internal/tracing/tracing.h\"\n#include \"po"
  },
  {
    "path": "c++/pod5_format/internal/tracing/tracing.h",
    "chars": 44,
    "preview": "#pragma once\n\n#define POD5_TRACE_FUNCTION()\n"
  },
  {
    "path": "c++/pod5_format/io_manager.cpp",
    "chars": 2607,
    "preview": "#include \"pod5_format/io_manager.h\"\n\n#ifdef __linux__\n#include <unistd.h>\n#endif\n\nnamespace pod5 {\n\n#ifdef __linux__\ncla"
  },
  {
    "path": "c++/pod5_format/io_manager.h",
    "chars": 2539,
    "preview": "#pragma once\n\n#include <arrow/buffer.h>\n#include <arrow/result.h>\n#include <arrow/status.h>\n\n#ifdef __linux__\n#include <"
  },
  {
    "path": "c++/pod5_format/memory_pool.cpp",
    "chars": 1016,
    "preview": "#include \"memory_pool.h\"\n\n#ifdef _WIN32\n#include <windows.h>\n#elif !defined(__FreeBSD__)\n#include <unistd.h>\n#endif\n\nnam"
  },
  {
    "path": "c++/pod5_format/memory_pool.h",
    "chars": 379,
    "preview": "#pragma once\n#include <arrow/memory_pool.h>\n\nnamespace pod5 {\n\n/// \\brief Find a memory pool that should be used by defa"
  },
  {
    "path": "c++/pod5_format/migration/migration.cpp",
    "chars": 1759,
    "preview": "#include \"pod5_format/migration/migration.h\"\n\n#include <random>\n\nnamespace pod5 {\n\nstatic bool registered_delete_at_exit"
  },
  {
    "path": "c++/pod5_format/migration/migration.h",
    "chars": 3376,
    "preview": "#pragma once\n\n#include \"pod5_format/internal/combined_file_utils.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_forma"
  },
  {
    "path": "c++/pod5_format/migration/migration_utils.h",
    "chars": 8936,
    "preview": "#pragma once\n\n#include \"pod5_format/internal/combined_file_utils.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_forma"
  },
  {
    "path": "c++/pod5_format/migration/v0_to_v1.cpp",
    "chars": 4722,
    "preview": "#include \"pod5_format/migration/migration.h\"\n#include \"pod5_format/migration/migration_utils.h\"\n#include \"pod5_format/ta"
  },
  {
    "path": "c++/pod5_format/migration/v1_to_v2.cpp",
    "chars": 5602,
    "preview": "#include \"pod5_format/migration/migration.h\"\n#include \"pod5_format/migration/migration_utils.h\"\n#include \"pod5_format/ta"
  },
  {
    "path": "c++/pod5_format/migration/v2_to_v3.cpp",
    "chars": 13984,
    "preview": "#include \"pod5_format/migration/migration.h\"\n#include \"pod5_format/migration/migration_utils.h\"\n#include \"pod5_format/ty"
  },
  {
    "path": "c++/pod5_format/migration/v3_to_v4.cpp",
    "chars": 2806,
    "preview": "#include \"pod5_format/migration/migration.h\"\n#include \"pod5_format/migration/migration_utils.h\"\n#include \"pod5_format/ta"
  },
  {
    "path": "c++/pod5_format/read_table_reader.cpp",
    "chars": 13211,
    "preview": "#include \"pod5_format/read_table_reader.h\"\n\n#include \"pod5_format/read_table_utils.h\"\n#include \"pod5_format/schema_metad"
  },
  {
    "path": "c++/pod5_format/read_table_reader.h",
    "chars": 4657,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/read_table_schema.h\"\n#include \"pod5_form"
  },
  {
    "path": "c++/pod5_format/read_table_schema.cpp",
    "chars": 3022,
    "preview": "#include \"pod5_format/read_table_schema.h\"\n\n#include \"pod5_format/schema_metadata.h\"\n#include \"pod5_format/types.h\"\n\nnam"
  },
  {
    "path": "c++/pod5_format/read_table_schema.h",
    "chars": 4129,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/schema_u"
  },
  {
    "path": "c++/pod5_format/read_table_utils.cpp",
    "chars": 598,
    "preview": "#include \"pod5_format/read_table_utils.h\"\n\n#include <algorithm>\n\nnamespace pod5 {\n\nReadIdSearchInput::ReadIdSearchInput("
  },
  {
    "path": "c++/pod5_format/read_table_utils.h",
    "chars": 11256,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/uuid.h\"\n\n#include <gsl/gsl-lite.hpp>\n\n#i"
  },
  {
    "path": "c++/pod5_format/read_table_writer.cpp",
    "chars": 5595,
    "preview": "#include \"pod5_format/read_table_writer.h\"\n\n#include \"pod5_format/file_output_stream.h\"\n#include \"pod5_format/internal/t"
  },
  {
    "path": "c++/pod5_format/read_table_writer.h",
    "chars": 3656,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/read_table_schema.h\"\n#include \"pod5_form"
  },
  {
    "path": "c++/pod5_format/read_table_writer_utils.cpp",
    "chars": 3520,
    "preview": "#include \"pod5_format/read_table_writer_utils.h\"\n\n#include \"pod5_format/read_table_schema.h\"\n\n#include <arrow/array/arra"
  },
  {
    "path": "c++/pod5_format/read_table_writer_utils.h",
    "chars": 4008,
    "preview": "#pragma once\n\n#include \"pod5_format/dictionary_writer.h\"\n#include \"pod5_format/expandable_buffer.h\"\n#include \"pod5_forma"
  },
  {
    "path": "c++/pod5_format/result.h",
    "chars": 218,
    "preview": "#pragma once\n\n#include <arrow/result.h>\n\nnamespace pod5 {\n\n/// pod5::Result is just an Arrow Result right now.\ntemplate "
  },
  {
    "path": "c++/pod5_format/run_info_table_reader.cpp",
    "chars": 10249,
    "preview": "#include \"pod5_format/run_info_table_reader.h\"\n\n#include \"pod5_format/schema_metadata.h\"\n#include \"pod5_format/schema_ut"
  },
  {
    "path": "c++/pod5_format/run_info_table_reader.h",
    "chars": 3917,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/read_table_utils.h\"\n#include \"pod5_forma"
  },
  {
    "path": "c++/pod5_format/run_info_table_schema.cpp",
    "chars": 2868,
    "preview": "#include \"pod5_format/run_info_table_schema.h\"\n\n#include \"pod5_format/schema_metadata.h\"\n#include \"pod5_format/types.h\"\n"
  },
  {
    "path": "c++/pod5_format/run_info_table_schema.h",
    "chars": 3046,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/schema_u"
  },
  {
    "path": "c++/pod5_format/run_info_table_writer.cpp",
    "chars": 4621,
    "preview": "#include \"pod5_format/run_info_table_writer.h\"\n\n#include \"pod5_format/file_output_stream.h\"\n#include \"pod5_format/intern"
  },
  {
    "path": "c++/pod5_format/run_info_table_writer.h",
    "chars": 3026,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/run_info"
  },
  {
    "path": "c++/pod5_format/schema_field_builder.h",
    "chars": 8227,
    "preview": "#pragma once\n\n#include \"pod5_format/dictionary_writer.h\"\n#include \"pod5_format/read_table_schema.h\"\n\n#include <arrow/arr"
  },
  {
    "path": "c++/pod5_format/schema_metadata.cpp",
    "chars": 3554,
    "preview": "#include \"pod5_format/schema_metadata.h\"\n\n#include \"pod5_format/uuid.h\"\n#include \"pod5_format/version.h\"\n\n#include <arro"
  },
  {
    "path": "c++/pod5_format/schema_metadata.h",
    "chars": 1914,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/uuid.h\"\n"
  },
  {
    "path": "c++/pod5_format/schema_utils.cpp",
    "chars": 2422,
    "preview": "#include \"pod5_format/schema_utils.h\"\n\nnamespace pod5 {\n\n/// \\brief Make a new schema for a read table to be written (wi"
  },
  {
    "path": "c++/pod5_format/schema_utils.h",
    "chars": 7983,
    "preview": "#pragma once\n\n#include \"pod5_format/schema_metadata.h\"\n\n#include <arrow/record_batch.h>\n#include <arrow/type.h>\n\nnamespa"
  },
  {
    "path": "c++/pod5_format/signal_builder.h",
    "chars": 5023,
    "preview": "#pragma once\n\n#include \"pod5_format/expandable_buffer.h\"\n#include \"pod5_format/signal_compression.h\"\n#include \"pod5_form"
  },
  {
    "path": "c++/pod5_format/signal_compression.cpp",
    "chars": 9021,
    "preview": "#include \"pod5_format/signal_compression.h\"\n\n#include \"pod5_format/svb16/decode.hpp\"\n#include \"pod5_format/svb16/encode."
  },
  {
    "path": "c++/pod5_format/signal_compression.h",
    "chars": 1077,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n\n#include <gsl/gsl-lite.hpp>\n\n"
  },
  {
    "path": "c++/pod5_format/signal_table_reader.cpp",
    "chars": 12925,
    "preview": "#include \"pod5_format/signal_table_reader.h\"\n\n#include \"pod5_format/schema_metadata.h\"\n#include \"pod5_format/signal_comp"
  },
  {
    "path": "c++/pod5_format/signal_table_reader.h",
    "chars": 4335,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/schema_m"
  },
  {
    "path": "c++/pod5_format/signal_table_schema.cpp",
    "chars": 2442,
    "preview": "#include \"pod5_format/signal_table_schema.h\"\n\n#include \"pod5_format/schema_utils.h\"\n#include \"pod5_format/types.h\"\n\n#inc"
  },
  {
    "path": "c++/pod5_format/signal_table_schema.h",
    "chars": 1068,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/signal_t"
  },
  {
    "path": "c++/pod5_format/signal_table_utils.h",
    "chars": 164,
    "preview": "#pragma once\n\nnamespace pod5 {\n\nusing SignalTableRowIndex = std::uint64_t;\n\nenum class SignalType {\n    UncompressedSign"
  },
  {
    "path": "c++/pod5_format/signal_table_writer.cpp",
    "chars": 7074,
    "preview": "#include \"pod5_format/signal_table_writer.h\"\n\n#include \"pod5_format/file_output_stream.h\"\n#include \"pod5_format/internal"
  },
  {
    "path": "c++/pod5_format/signal_table_writer.h",
    "chars": 4509,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/signal_b"
  },
  {
    "path": "c++/pod5_format/svb16/common.hpp",
    "chars": 976,
    "preview": "#pragma once\n\n#if __cplusplus >= 201703L\n#define SVB16_IF_CONSTEXPR if constexpr\n#else\n#define SVB16_IF_CONSTEXPR if\n#en"
  },
  {
    "path": "c++/pod5_format/svb16/decode.hpp",
    "chars": 2510,
    "preview": "#pragma once\n\n#include \"common.hpp\"\n#include \"decode_scalar.hpp\"\n#include \"svb16.h\"  // svb16_key_length\n\n#include <type"
  },
  {
    "path": "c++/pod5_format/svb16/decode_scalar.hpp",
    "chars": 1912,
    "preview": "#pragma once\n\n#include \"common.hpp\"\n\n#include <gsl/gsl-lite.hpp>\n\n#include <cassert>\n#include <cstddef>\n#include <cstdin"
  },
  {
    "path": "c++/pod5_format/svb16/decode_x64.hpp",
    "chars": 10441,
    "preview": "#pragma once\n\n#include \"common.hpp\"\n#include \"decode_scalar.hpp\"\n#include \"intrinsics.hpp\"\n#include \"shuffle_tables.hpp\""
  },
  {
    "path": "c++/pod5_format/svb16/encode.hpp",
    "chars": 702,
    "preview": "#pragma once\n\n#include \"common.hpp\"\n#include \"encode_scalar.hpp\"\n#include \"svb16.h\"  // svb16_key_length\n#ifdef SVB16_X6"
  },
  {
    "path": "c++/pod5_format/svb16/encode_scalar.hpp",
    "chars": 1776,
    "preview": "#pragma once\n\n#include \"common.hpp\"\n\n#include <cstddef>\n#include <cstdint>\n#include <cstring>\n\nnamespace svb16 {\nnamespa"
  },
  {
    "path": "c++/pod5_format/svb16/encode_x64.hpp",
    "chars": 3907,
    "preview": "#pragma once\n\n#include \"common.hpp\"\n#include \"encode_scalar.hpp\"\n#include \"intrinsics.hpp\"\n#include \"shuffle_tables.hpp\""
  },
  {
    "path": "c++/pod5_format/svb16/generate_shuffle_tables.py",
    "chars": 1435,
    "preview": "def encode_table_row(control):\n    table = []\n    for i in range(7):\n        offset = i * 2\n        # first byte\n       "
  },
  {
    "path": "c++/pod5_format/svb16/intrinsics.hpp",
    "chars": 1647,
    "preview": "#pragma once\n\n#include \"common.hpp\"  // architecture macros\n\n#if defined(_MSC_VER)\n#include <intrin.h>\n#elif defined(__G"
  },
  {
    "path": "c++/pod5_format/svb16/shuffle_tables.hpp",
    "chars": 58335,
    "preview": "#pragma once\n#include \"common.hpp\"  // arch macros\n\n#include <cstdint>\n\n#ifdef SVB16_X64\nstatic constexpr uint8_t g_enco"
  },
  {
    "path": "c++/pod5_format/svb16/simd_detect_x64.hpp",
    "chars": 1470,
    "preview": "#pragma once\n\n#include \"common.hpp\"  // architecture macros\n\n#if defined(SVB16_X64)\n\n#ifdef _MSC_VER\n#include <intrin.h>"
  },
  {
    "path": "c++/pod5_format/svb16/streamvbytedelta_decode_16.c",
    "chars": 2064,
    "preview": "#include \"streamvbyte_isadetection.h\"\n#include \"streamvbytedelta.h\"\n\n#include <string.h>  // for memcpy\n\nstatic inline u"
  },
  {
    "path": "c++/pod5_format/svb16/streamvbytedelta_encode_16.c",
    "chars": 2223,
    "preview": "#include \"streamvbyte_isadetection.h\"\n#include \"streamvbytedelta.h\"\n\n#include <stdio.h>\n#include <string.h>  // for memc"
  },
  {
    "path": "c++/pod5_format/svb16/streamvbytedelta_x64_decode_16.c",
    "chars": 7088,
    "preview": "#include \"streamvbyte_isadetection.h\"\n#include \"streamvbyte_shuffle_tables_decode_16.h\"\n\n#include <string.h>  // for mem"
  },
  {
    "path": "c++/pod5_format/svb16/streamvbytedelta_x64_encode_16.c",
    "chars": 2973,
    "preview": "\n#include \"streamvbyte_isadetection.h\"\n#include \"streamvbyte_shuffle_tables_encode_16.h\"\n\n#include <stdio.h>\n#include <s"
  },
  {
    "path": "c++/pod5_format/svb16/svb16.c",
    "chars": 0,
    "preview": ""
  },
  {
    "path": "c++/pod5_format/svb16/svb16.h",
    "chars": 618,
    "preview": "#ifndef SVB16_H\n#define SVB16_H\n\n#include <stdint.h>\n\n#if defined(__cplusplus)\nextern \"C\" {\n#endif\n\n/// Get the number o"
  },
  {
    "path": "c++/pod5_format/table_reader.cpp",
    "chars": 2355,
    "preview": "#include \"pod5_format/table_reader.h\"\n\n#include <arrow/ipc/reader.h>\n#include <arrow/record_batch.h>\n#include <arrow/uti"
  },
  {
    "path": "c++/pod5_format/table_reader.h",
    "chars": 2004,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/schema_metadata.h\"\n\n#include <memory>\n\nn"
  },
  {
    "path": "c++/pod5_format/thread_pool.cpp",
    "chars": 5970,
    "preview": "#include \"pod5_format/thread_pool.h\"\n\n#include <atomic>\n#include <cassert>\n#include <condition_variable>\n#include <deque"
  },
  {
    "path": "c++/pod5_format/thread_pool.h",
    "chars": 934,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n\n#include <functional>\n#include <memory>\n\nnamespace pod5 {\n\ncl"
  },
  {
    "path": "c++/pod5_format/tuple_utils.h",
    "chars": 1018,
    "preview": "#pragma once\n\n#include <tuple>\n#include <utility>\n\nnamespace pod5 { namespace detail {\n\ntemplate <typename T, typename F"
  },
  {
    "path": "c++/pod5_format/types.cpp",
    "chars": 5307,
    "preview": "#include \"pod5_format/types.h\"\n\n#include <arrow/array/array_binary.h>\n#include <arrow/array/builder_binary.h>\n#include <"
  },
  {
    "path": "c++/pod5_format/types.h",
    "chars": 3392,
    "preview": "#pragma once\n\n#include \"pod5_format/pod5_format_export.h\"\n#include \"pod5_format/result.h\"\n#include \"pod5_format/uuid.h\"\n"
  },
  {
    "path": "c++/pod5_format/uuid.h",
    "chars": 10593,
    "preview": "#pragma once\n\n// This file contains code from https://github.com/mariusbancila/stduuid/ which has the following\n// licen"
  },
  {
    "path": "c++/pod5_format/version.h.in",
    "chars": 292,
    "preview": "#pragma once\n\n#include <string>\n\nnamespace pod5 {\n\nstd::uint16_t const Pod5MajorVersion = @POD5_VERSION_MAJOR@;\nstd::uin"
  },
  {
    "path": "c++/pod5_format_pybind/CMakeLists.txt",
    "chars": 2181,
    "preview": "\npybind11_add_module(pod5_format_pybind\n    api.h\n    bindings.cpp\n    utils.h\n    subset.cpp\n    subset.h\n\n    repack/r"
  },
  {
    "path": "c++/pod5_format_pybind/_version.py.in",
    "chars": 205,
    "preview": "# This file is auto generated by cmake during compilation\n__version__ = version = \"@POD5_FULL_VERSION@\"\n__version_tuple_"
  },
  {
    "path": "c++/pod5_format_pybind/api.h",
    "chars": 24772,
    "preview": "#pragma once\n\n#include \"pod5_format/async_signal_loader.h\"\n#include \"pod5_format/c_api.h\"\n#include \"pod5_format/file_rea"
  },
  {
    "path": "c++/pod5_format_pybind/bindings.cpp",
    "chars": 7087,
    "preview": "#include \"api.h\"\n#include \"pod5_format/c_api.h\"\n#include \"repack/repack_output.h\"\n#include \"repack/repacker.h\"\n#include "
  },
  {
    "path": "c++/pod5_format_pybind/build_wheel.cmake",
    "chars": 1448,
    "preview": "\nmessage(\"Building python lib-pod5 wheel using ${PYTHON_EXECUTABLE}\")\nmessage(\"  project dir ${PYTHON_PROJECT_DIR}\")\nmes"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repack_functions.h",
    "chars": 13049,
    "preview": "#pragma once\n\n#include \"pod5_format/internal/tracing/tracing.h\"\n#include \"pod5_format/read_table_reader.h\"\n#include \"pod"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repack_output.cpp",
    "chars": 12035,
    "preview": "#include \"repack_output.h\"\n\n#include \"pod5_format/internal/tracing/tracing.h\"\n#include \"repack_functions.h\"\n\n#include <i"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repack_output.h",
    "chars": 2269,
    "preview": "#pragma once\n\n#include \"pod5_format/file_writer.h\"\n#include \"pod5_format/thread_pool.h\"\n#include \"repack_states.h\"\n\n#inc"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repack_states.h",
    "chars": 2358,
    "preview": "#pragma once\n\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format/signal_builder.h\"\n\n#include <arrow/array/builde"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repack_utils.h",
    "chars": 5462,
    "preview": "#pragma once\n\n#include \"pod5_format/read_table_reader.h\"\n\n#include <arrow/array/array_dict.h>\n\n#include <mutex>\n#include"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repacker.cpp",
    "chars": 4608,
    "preview": "#include \"repacker.h\"\n\n#include \"pod5_format/internal/tracing/tracing.h\"\n#include \"repack_output.h\"\n#include \"repack_sta"
  },
  {
    "path": "c++/pod5_format_pybind/repack/repacker.h",
    "chars": 2168,
    "preview": "#pragma once\n\n#include \"pod5_format_pybind/api.h\"\n\n#include <pybind11/pybind11.h>\n\n#include <memory>\n#include <set>\n#inc"
  },
  {
    "path": "c++/pod5_format_pybind/subset.cpp",
    "chars": 18545,
    "preview": "#include \"subset.h\"\n\n#include <algorithm>\n#include <chrono>\n#include <cmath>\n#include <cstddef>\n#include <cstdlib>\n#incl"
  },
  {
    "path": "c++/pod5_format_pybind/subset.h",
    "chars": 365,
    "preview": "#include <pybind11/stl/filesystem.h>\n\n#include <filesystem>\n#include <map>\n#include <string>\n#include <vector>\n\nvoid sub"
  },
  {
    "path": "c++/pod5_format_pybind/utils.h",
    "chars": 1472,
    "preview": "#pragma once\n\n#include \"pod5_format/result.h\"\n\ninline void raise_error(arrow::Status const & status)\n{\n    throw std::ru"
  },
  {
    "path": "c++/test/CMakeLists.txt",
    "chars": 977,
    "preview": "\nadd_executable(pod5_unit_tests\n    main.cpp\n    c_api_null_input.cpp\n    c_api_test_utils.h\n    c_api_tests.cpp\n    c_a"
  },
  {
    "path": "c++/test/TemporaryDirectory.h",
    "chars": 2622,
    "preview": "#pragma once\n\n#include \"pod5_format/uuid.h\"\n\n#include <filesystem>\n\nnamespace ont { namespace testutils {\n\nstatic std::s"
  },
  {
    "path": "c++/test/c_api_build_test.c",
    "chars": 88,
    "preview": "#include \"pod5_format/c_api.h\"\n\n// Build check to verify a c file can include the c_api\n"
  },
  {
    "path": "c++/test/c_api_null_input.cpp",
    "chars": 23203,
    "preview": "#include \"c_api_test_utils.h\"\n#include \"pod5_format/c_api.h\"\n#include \"utils.h\"\n\n#include <bit>\n#include <numeric>\n#incl"
  },
  {
    "path": "c++/test/c_api_test_utils.h",
    "chars": 2366,
    "preview": "#pragma once\n\n#include \"pod5_format/c_api.h\"\n\n#include <catch2/catch.hpp>\n\n#include <string>\n\n#define CHECK_POD5_OK(stat"
  },
  {
    "path": "c++/test/c_api_tests.cpp",
    "chars": 35004,
    "preview": "#include \"pod5_format/c_api.h\"\n\n#include \"c_api_test_utils.h\"\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format"
  },
  {
    "path": "c++/test/file_reader_writer_tests.cpp",
    "chars": 35859,
    "preview": "#include \"pod5_format/async_signal_loader.h\"\n#include \"pod5_format/file_reader.h\"\n#include \"pod5_format/file_writer.h\"\n#"
  },
  {
    "path": "c++/test/main.cpp",
    "chars": 54,
    "preview": "#define CATCH_CONFIG_MAIN\n#include <catch2/catch.hpp>\n"
  },
  {
    "path": "c++/test/output_stream_tests.cpp",
    "chars": 4354,
    "preview": "#include \"pod5_format/internal/async_output_stream.h\"\n#include \"pod5_format/internal/linux_output_stream.h\"\n#include \"te"
  },
  {
    "path": "c++/test/read_table_tests.cpp",
    "chars": 9365,
    "preview": "#include \"pod5_format/internal/async_output_stream.h\"\n#include \"pod5_format/read_table_reader.h\"\n#include \"pod5_format/r"
  },
  {
    "path": "c++/test/read_table_writer_utils_tests.cpp",
    "chars": 1665,
    "preview": "#include \"pod5_format/read_table_writer_utils.h\"\n\n#include \"test_utils.h\"\n#include \"utils.h\"\n\n#include <arrow/array/arra"
  },
  {
    "path": "c++/test/run_info_table_tests.cpp",
    "chars": 5266,
    "preview": "#include \"pod5_format/internal/async_output_stream.h\"\n#include \"pod5_format/run_info_table_reader.h\"\n#include \"pod5_form"
  },
  {
    "path": "c++/test/schema_tests.cpp",
    "chars": 1145,
    "preview": "#include \"pod5_format/schema_metadata.h\"\n#include \"test_utils.h\"\n\n#include <catch2/catch.hpp>\n\nSCENARIO(\"Version Tests\")"
  },
  {
    "path": "c++/test/signal_compression_tests.cpp",
    "chars": 957,
    "preview": "#include \"pod5_format/signal_compression.h\"\n\n#include \"test_utils.h\"\n#include \"utils.h\"\n\n#include <arrow/buffer.h>\n#incl"
  },
  {
    "path": "c++/test/signal_table_tests.cpp",
    "chars": 5752,
    "preview": "#include \"pod5_format/internal/async_output_stream.h\"\n#include \"pod5_format/schema_metadata.h\"\n#include \"pod5_format/sig"
  },
  {
    "path": "c++/test/svb16_scalar_tests.cpp",
    "chars": 2671,
    "preview": "#include \"pod5_format/svb16/decode.hpp\"\n#include \"pod5_format/svb16/encode.hpp\"\n\n#include <catch2/catch.hpp>\n\n#include <"
  },
  {
    "path": "c++/test/svb16_x64_tests.cpp",
    "chars": 3328,
    "preview": "#include \"pod5_format/svb16/decode.hpp\"\n#include \"pod5_format/svb16/encode.hpp\"\n\n#include <catch2/catch.hpp>\n\n#include <"
  },
  {
    "path": "c++/test/test_utils.h",
    "chars": 2255,
    "preview": "#pragma once\n\n#include <arrow/result.h>\n#include <arrow/status.h>\n#include <catch2/catch.hpp>\n\ntemplate <typename T>\nstr"
  },
  {
    "path": "c++/test/thread_pool_tests.cpp",
    "chars": 3053,
    "preview": "#include \"pod5_format/thread_pool.h\"\n\n#include <catch2/catch.hpp>\n\n#include <condition_variable>\n#include <mutex>\n#inclu"
  },
  {
    "path": "c++/test/utils.h",
    "chars": 1515,
    "preview": "#pragma once\n\n#include \"pod5_format/read_table_utils.h\"\n#include \"test_utils.h\"\n\n#include <arrow/result.h>\n#include <arr"
  },
  {
    "path": "c++/test/uuid_tests.cpp",
    "chars": 8973,
    "preview": "// This file contains code from https://github.com/mariusbancila/stduuid/ which has the following\n// license:\n//\n//   MI"
  },
  {
    "path": "ci/docker/Dockerfile.conda",
    "chars": 44,
    "preview": "FROM condaforge/mambaforge:latest\nWORKDIR /\n"
  },
  {
    "path": "ci/docker/Dockerfile.py39.arm64",
    "chars": 434,
    "preview": "from git.oxfordnanolabs.local:4567/minknow/images/build-aarch64-gcc9\n\nRUN yum groupinstall \"Development Tools\" -y\nRUN yu"
  },
  {
    "path": "ci/docker/Dockerfile.py39.x64",
    "chars": 433,
    "preview": "from git.oxfordnanolabs.local:4567/minknow/images/build-x86_64-gcc9\n\nRUN yum groupinstall \"Development Tools\" -y\nRUN yum"
  },
  {
    "path": "ci/generate_coverage_report.sh",
    "chars": 1959,
    "preview": "#!/bin/bash -e\n\n# Parse args.\nif [ $# -ne 1 ]; then\n    echo \"Usage: $0 build_dir\"\n    exit 1\nfi\nbuild_dir=$(realpath \"$"
  },
  {
    "path": "ci/get_tag_version.cmake",
    "chars": 126,
    "preview": "set(CANONICAL_TAG_BUILD TRUE)\ninclude(\"${CMAKE_CURRENT_LIST_DIR}/../cmake/POD5Version.cmake\")\nmessage(\"${POD5_FULL_VERSI"
  },
  {
    "path": "ci/gitlab-ci-common.yml",
    "chars": 25281,
    "preview": "variables:\n    CONAN_USER: nanopore\n    CONAN_CHANNEL: stable\n    CONAN_REFERENCE: '.'\n    # Location of the .conan dir:"
  },
  {
    "path": "ci/install.sh",
    "chars": 639,
    "preview": "#!/bin/bash\n\nset -o errexit\nset -o pipefail\nset -o nounset\n# set -o xtrace\n\n# Tar up the archive build:\n(\n    cmake -DCM"
  },
  {
    "path": "ci/package.sh",
    "chars": 898,
    "preview": "#!/bin/bash\n\nset -o errexit\nset -o pipefail\nset -o nounset\n# set -o xtrace\n\noutput_sku=$1\nauditwheel_platform=\nif [ $# -"
  },
  {
    "path": "ci/unpack_libs_for_python.sh",
    "chars": 713,
    "preview": "#!/bin/bash\n\ninput_dir=$1\noutput_dir=$2\n\necho \"Unpacking builds from $input_dir to $output_dir\"\n\nfile_regex=\".*/lib_pod5"
  },
  {
    "path": "cmake/BuildFlatBuffers.cmake",
    "chars": 15842,
    "preview": "# Copyright 2015 Google Inc. All rights reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# "
  },
  {
    "path": "cmake/Findzstd.cmake",
    "chars": 2781,
    "preview": "find_path(ZSTD_INCLUDE_DIR\n    NAMES zstd.h\n    PATHS\n        ${CONAN_INCLUDE_DIRS_RELEASE}\n        ${CONAN_INCLUDE_DIRS"
  },
  {
    "path": "cmake/conan_provider.cmake",
    "chars": 29097,
    "preview": "# The MIT License (MIT)\n#\n# Copyright (c) 2024 JFrog\n#\n# Permission is hereby granted, free of charge, to any person obt"
  },
  {
    "path": "cmake/pod5_fuzz.cmake",
    "chars": 547,
    "preview": "if (NOT CMAKE_CXX_COMPILER_ID MATCHES \"Clang\")\n    message(FATAL_ERROR\n        \"Only LLVM based compilers are supported "
  },
  {
    "path": "cmake/pod5_packaging.cmake",
    "chars": 360,
    "preview": "\nset(CPACK_PACKAGE_NAME \"lib_pod5\")\nset(CPACK_PACKAGE_VENDOR \"Oxford Nanopore\")\nset(CPACK_VERBATIM_VARIABLES true)\nset(C"
  },
  {
    "path": "cmake/presets/conan-build-options.json",
    "chars": 1227,
    "preview": "{\n    \"version\": 4,\n    \"configurePresets\": [\n        {\n            \"name\": \"conan2-debug\",\n            \"binaryDir\": \"${"
  },
  {
    "path": "cmake/presets/conan-profiles.json",
    "chars": 3684,
    "preview": "{\n    \"version\": 4,\n    \"configurePresets\": [\n        {\n            \"name\": \"conan2-gcc9-x86_64-profile\",\n            \"h"
  },
  {
    "path": "cmake/presets/conan-provider.json",
    "chars": 505,
    "preview": "{\n    \"version\": 4,\n    \"configurePresets\": [\n        {\n            \"name\": \"conan2-provider\",\n            \"hidden\": tru"
  },
  {
    "path": "conanfile.py",
    "chars": 7321,
    "preview": "from conan import ConanFile\nfrom conan.tools.cmake import CMakeToolchain, CMake, CMakeDeps\nfrom conan.tools.files import"
  },
  {
    "path": "docs/DESIGN.md",
    "chars": 3377,
    "preview": "POD5 File Format Design Details\n==============================\n\n## Summary\n\nThis file format has the following design go"
  },
  {
    "path": "docs/README.md",
    "chars": 1083,
    "preview": "Design documentation for POD5\n============================\n\nThe POD5 file format has been specifically designed to be su"
  },
  {
    "path": "docs/SPECIFICATION.md",
    "chars": 8726,
    "preview": "POD5 Format Specification\n=========================\n\n## Overview\n\nThe file format is, at its core, a collection of Apach"
  }
]

// ... and 97 more files (download for full content)