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Lib POD5 Reference

c++ bindings for pod5_format

CleanupError 

CleanupError()

description instance-attribute 

description: str

file_path instance-attribute 

file_path: str

EmbeddedFileData 

EmbeddedFileData(*args, **kwargs)

file_path property 

file_path: str

length property 

length: int

offset property 

offset: int

FileWriter 

FileWriter(*args, **kwargs)

add_end_reason 

add_end_reason(end_reason_enum: int) -> int

add_pore 

add_pore(pore_type: str) -> int

add_reads 

add_reads(
    count: int,
    read_ids: NDArray[uint8],
    read_numbers: NDArray[uint32],
    start_samples: NDArray[uint64],
    channels: NDArray[uint16],
    wells: NDArray[uint8],
    pore_types: NDArray[int16],
    calibration_offsets: NDArray[float32],
    calibration_scales: NDArray[float32],
    median_befores: NDArray[float32],
    end_reasons: NDArray[int16],
    end_reason_forceds: NDArray[bool_],
    run_infos: NDArray[int16],
    num_minknow_events: NDArray[uint64],
    tracked_scaling_scales: NDArray[float32],
    tracked_scaling_shifts: NDArray[float32],
    predicted_scaling_scales: NDArray[float32],
    predicted_scaling_shifts: NDArray[float32],
    num_reads_since_mux_changes: NDArray[uint32],
    time_since_mux_changes: NDArray[float32],
    open_pore_levels: NDArray[float32],
    signals: List[NDArray[int16]],
) -> None

add_reads_pre_compressed 

add_reads_pre_compressed(
    count: int,
    read_ids: NDArray[uint8],
    read_numbers: NDArray[uint32],
    start_samples: NDArray[uint64],
    channels: NDArray[uint16],
    wells: NDArray[uint8],
    pore_types: NDArray[int16],
    calibration_offsets: NDArray[float32],
    calibration_scales: NDArray[float32],
    median_befores: NDArray[float32],
    end_reasons: NDArray[int16],
    end_reason_forceds: NDArray[bool_],
    run_infos: NDArray[int16],
    num_minknow_events: NDArray[uint64],
    tracked_scaling_scales: NDArray[float32],
    tracked_scaling_shifts: NDArray[float32],
    predicted_scaling_scales: NDArray[float32],
    predicted_scaling_shifts: NDArray[float32],
    num_reads_since_mux_changes: NDArray[uint32],
    time_since_mux_changes: NDArray[float32],
    open_pore_levels: NDArray[float32],
    signal_chunks: List[NDArray[uint8]],
    signal_chunk_lengths: NDArray[uint32],
    signal_chunk_counts: NDArray[uint32],
) -> None

add_run_info 

add_run_info(
    acquisition_id: str,
    acquisition_start_time: int,
    adc_max: int,
    adc_min: int,
    context_tags: List[Tuple[str, str]],
    experiment_name: str,
    flow_cell_id: str,
    flow_cell_product_code: str,
    protocol_name: str,
    protocol_run_id: str,
    protocol_start_time: int,
    sample_id: str,
    sample_rate: int,
    sequencing_kit: str,
    sequencer_position: str,
    sequencer_position_type: str,
    software: str,
    system_name: str,
    system_type: str,
    tracking_id: List[Tuple[str, str]],
) -> int

close 

close() -> None

FileWriterOptions 

FileWriterOptions(*args, **kwargs)

max_signal_chunk_size instance-attribute 

max_signal_chunk_size: int

read_table_batch_size instance-attribute 

read_table_batch_size: int

signal_compression_type instance-attribute 

signal_compression_type: Any

signal_table_batch_size instance-attribute 

signal_table_batch_size: int

Pod5AsyncSignalLoader 

Pod5AsyncSignalLoader(*args, **kwargs)

release_next_batch 

release_next_batch() -> Pod5SignalCacheBatch

Pod5FileReader 

Pod5FileReader(*args, **kwargs)

batch_get_signal 

batch_get_signal(get_samples: bool, get_sample_count: bool) -> Pod5AsyncSignalLoader

batch_get_signal_batches 

batch_get_signal_batches(
    get_samples: bool, get_samples_count: bool, batches: NDArray[uint32]
) -> Pod5AsyncSignalLoader

batch_get_signal_selection 

batch_get_signal_selection(
    get_samples: bool,
    get_sample_count: bool,
    batch_counts: NDArray[uint32],
    batch_rows: NDArray[uint32],
) -> Pod5AsyncSignalLoader

close 

close() -> None

get_file_read_table_location 

get_file_read_table_location() -> EmbeddedFileData

get_file_run_info_table_location 

get_file_run_info_table_location() -> EmbeddedFileData

get_file_signal_table_location 

get_file_signal_table_location() -> EmbeddedFileData

get_file_version_pre_migration 

get_file_version_pre_migration() -> str

plan_traversal 

plan_traversal(
    read_id_data: NDArray[uint8],
    batch_counts: NDArray[uint32],
    batch_rows: NDArray[uint32],
) -> int

Pod5RepackerOutput 

Pod5RepackerOutput(*args, **kwargs)

Pod5SignalCacheBatch 

Pod5SignalCacheBatch(*args, **kwargs)

batch_index property 

batch_index: int

sample_count property 

sample_count: NDArray[uint64]

samples property 

samples: List[NDArray[int16]]

RecoverFileOptions 

RecoverFileOptions()

cleanup instance-attribute 

cleanup: bool

file_writer_options instance-attribute 

file_writer_options: FileWriterOptions

RecoveredRowCounts 

RecoveredRowCounts()

reads instance-attribute 

reads: int

run_info instance-attribute 

run_info: int

signal instance-attribute 

signal: int

RecoveryDetails 

RecoveryDetails()

cleanup_errors instance-attribute 

cleanup_errors: list[CleanupError]

row_counts instance-attribute 

row_counts: RecoveredRowCounts

Repacker 

Repacker()

is_complete property 

is_complete: bool

open_file_readers property 

open_file_readers: int

reads_completed property 

reads_completed: int

add_all_reads_to_output 

add_all_reads_to_output(output: Pod5RepackerOutput, input: Pod5FileReader) -> None

add_output 

add_output(output: FileWriter, check_duplicate_read_ids: bool) -> Pod5RepackerOutput

add_selected_reads_to_output 

add_selected_reads_to_output(
    output: Pod5RepackerOutput,
    input: Pod5FileReader,
    batch_counts: NDArray[uint32],
    all_batch_rows: NDArray[uint32],
) -> None

finish 

finish() -> None

compress_signal 

compress_signal(signal: NDArray[int16], compressed_signal_out: NDArray[uint8]) -> int

create_file 

create_file(
    src_filename: str, writer_name: str, options: Optional[FileWriterOptions]
) -> FileWriter

decompress_signal 

decompress_signal(
    compressed_signal: Union[NDArray[uint8], memoryview], signal_out: NDArray[int16]
) -> None

format_read_id_to_str 

format_read_id_to_str(read_id_data_out: NDArray[uint8]) -> List[str]

get_error_string 

get_error_string() -> str

load_read_id_iterable 

load_read_id_iterable(read_ids_str: Iterable, read_id_data_out: NDArray[uint8]) -> int

open_file 

open_file(filename: str) -> Pod5FileReader

recover_file 

recover_file(
    src_filename: str, dest_filename: str, options: Optional[RecoverFileOptions]
) -> RecoveryDetails

update_file 

update_file(reader: Pod5FileReader, output: str)

vbz_compressed_signal_max_size 

vbz_compressed_signal_max_size(sample_count: int) -> int