Index

_

__init__() (ArrowTableHandle method) (BaseRead method) (Calibration method) (CompressedRead method) (EndReason method) (OutputHandler method) (Pore method) (QueueManager method) (Read method) (Reader method) (ReadRecord method) (ReadRecordBatch method) (Repacker method) (RunInfo method) (ShiftScalePair method) (StatusMonitor method), [1] (Writer method)

A

acquisition_id (RunInfo attribute) acquisition_start_time (RunInfo attribute) adc_max (RunInfo attribute) adc_min (RunInfo attribute) add() (Writer method) add_all_reads_to_output() (Repacker method), [1] add_end_reason() (FileWriter method) add_output() (Repacker method), [1] add_pore() (FileWriter method) add_read() (Writer method)

add_reads() (FileWriter method) (Writer method) add_reads_pre_compressed() (FileWriter method) add_run_info() (FileWriter method) add_selected_reads_to_output() (Repacker method), [1] ArrowTableHandle (class in pod5.reader) assert_filename_template() (in module pod5.tools.pod5_subset) assert_no_duplicate_reads() (in module pod5.tools.pod5_merge) assert_overwrite_ok() (in module pod5.tools.pod5_subset) await_data() (QueueManager method) await_request() (QueueManager method)

B

BaseRead (class in pod5.pod5_types) batch_count (Reader property) batch_get_signal() (Pod5FileReader method) batch_get_signal_batches() (Pod5FileReader method) batch_get_signal_selection() (Pod5FileReader method) batch_index (Pod5SignalCacheBatch property) (SignalRowInfo property) batch_row_index (SignalRowInfo property) batches_completed (Repacker property), [1] batches_requested (Repacker property), [1]

built-in function compress_signal() create_file() decompress_signal() format_read_id_to_str() get_error_string() load_read_id_iterable() open_file() vbz_compressed_signal_max_size() byte_count (ReadRecord property) (SignalRowInfo property)

C

cached_sample_count_column (ReadRecordBatch property) cached_samples_column (ReadRecordBatch property) calculate_transfers() (in module pod5.tools.pod5_subset) calibrate_signal_array() (ReadRecord method) calibration (BaseRead attribute) Calibration (class in pod5.pod5_types) calibration (ReadRecord property) calibration_digitisation (ReadRecord property) calibration_offset (ReadRecordV3Columns property) calibration_range (ReadRecord property) calibration_scale (ReadRecordV3Columns property) channel (Pore attribute) (ReadRecordV3Columns property) close() (ArrowTableHandle method) (FileWriter method) (Pod5FileReader method) (Reader method) (StatusMonitor method) (Writer method)

close_all() (OutputHandler method) columns (ReadRecordBatch property) compress_signal() built-in function CompressedRead (class in pod5.pod5_types) contains() (Writer method) context_tags (RunInfo attribute) convert_datetime_as_epoch_ms() (in module pod5.tools.pod5_convert_from_fast5) convert_fast5_end_reason() (in module pod5.tools.pod5_convert_from_fast5) convert_fast5_file() (in module pod5.tools.pod5_convert_from_fast5) convert_fast5_file_chunk() (in module pod5.tools.pod5_convert_from_fast5) convert_fast5_files() (in module pod5.tools.pod5_convert_from_fast5) convert_fast5_read() (in module pod5.tools.pod5_convert_from_fast5) convert_from_fast5() (in module pod5.tools.pod5_convert_from_fast5) convert_pod5_to_fast5() (in module pod5.tools.pod5_convert_to_fast5) convert_run_info() (in module pod5.tools.pod5_convert_from_fast5) convert_to_fast5() (in module pod5.tools.pod5_convert_to_fast5) create_default_filename_template() (in module pod5.tools.pod5_subset) create_file() built-in function

D

DATA_SERVICE_UNBLOCK_MUX_CHANGE (EndReasonEnum attribute) decode_str() (in module pod5.tools.pod5_convert_from_fast5) decompress_signal() built-in function decompressed_signal (CompressedRead property)

deprecation_warning() (in module pod5.api_utils) do_debug_command() (in module pod5.tools.pod5_inspect) do_read_command() (in module pod5.tools.pod5_inspect) do_reads_command() (in module pod5.tools.pod5_inspect) do_summary_command() (in module pod5.tools.pod5_inspect) dump_run_info() (in module pod5.tools.pod5_inspect)

E

EmbeddedFileData (built-in class) end_reason (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) end_reason_forced (ReadRecordV3Columns property) end_reason_index (ReadRecord property)

EndReason (class in pod5.pod5_types) EndReasonEnum (class in pod5.pod5_types) enqueue_data() (QueueManager method) enqueue_exception() (QueueManager method) enqueue_input() (QueueManager method) enqueue_request() (QueueManager method) experiment_name (RunInfo attribute)

F

file_identifier (Reader property) file_path (EmbeddedFileData property) file_version (Reader property) file_version_pre_migration (Reader property) FileWriter (built-in class) FileWriterOptions (built-in class) filter_pod5() (in module pod5.tools.pod5_filter) find() (Writer method) finish() (Repacker method), [1] flow_cell_id (RunInfo attribute)

flow_cell_product_code (RunInfo attribute) force_type_and_default() (in module pod5.writer) forced (EndReason attribute) format_read_id_to_str() built-in function format_read_ids() (in module pod5.api_utils) format_shift_scale_pair() (in module pod5.tools.pod5_inspect) format_shift_scale_pair_num() (in module pod5.tools.pod5_inspect) formatted_sample_count (StatusMonitor property) from_range() (Calibration class method) from_reason_with_default_forced() (EndReason class method)

G

get_batch() (Reader method) get_error_string() built-in function get_exception() (QueueManager method) get_file_read_table_location() (Pod5FileReader method)

get_file_run_info_table_location() (Pod5FileReader method) get_file_signal_table_location() (Pod5FileReader method) get_input() (QueueManager method) get_read() (ReadRecordBatch method) get_read_from_fast5() (in module pod5.tools.pod5_convert_from_fast5) get_writer() (OutputHandler method)

H

handle_exception() (in module pod5.tools.pod5_convert_from_fast5)

has_cached_signal (ReadRecord property)

I

increment() (StatusMonitor method) increment_reads() (StatusMonitor method) inner_file_reader (Reader property) inspect_pod5() (in module pod5.tools.pod5_inspect) is_complete (Repacker property), [1]

is_disable_pbar() (in module pod5.tools.utils) is_multi_read_fast5() (in module pod5.tools.pod5_convert_from_fast5) is_pod5_debug() (in module pod5.tools.utils) is_vbz_compressed (Reader property) issue_not_multi_read_exception() (in module pod5.tools.pod5_convert_from_fast5) iterate_inputs() (in module pod5.tools.utils)

L

launch_subsetting() (in module pod5.tools.pod5_subset) length (EmbeddedFileData property) load_read_id_iterable() built-in function

logged() (in module pod5.tools.pod5_convert_from_fast5) logged_all() (in module pod5.tools.pod5_convert_from_fast5)

M

main() (in module pod5.tools.pod5_convert_from_fast5) (in module pod5.tools.pod5_convert_to_fast5) (in module pod5.tools.pod5_filter) (in module pod5.tools.pod5_inspect) (in module pod5.tools.pod5_merge) (in module pod5.tools.pod5_repack) (in module pod5.tools.pod5_subset) (in module pod5.tools.pod5_update) map_to_tuples() (in module pod5.writer) max_signal_chunk_size (FileWriterOptions attribute) median_before (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) merge_pod5() (in module pod5.tools.pod5_merge) module pod5 pod5.api_utils pod5.pod5_types pod5.reader pod5.repack pod5.signal_tools pod5.tools.pod5_convert_from_fast5 pod5.tools.pod5_convert_to_fast5 pod5.tools.pod5_filter pod5.tools.pod5_inspect pod5.tools.pod5_merge pod5.tools.pod5_repack pod5.tools.pod5_subset pod5.tools.pod5_update pod5.tools.utils pod5.writer

MUX_CHANGE (EndReasonEnum attribute)

N

name (EndReason property) num_minknow_events (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) num_reads (Reader property) (ReadRecordBatch property)

num_reads_since_mux_change (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) num_samples (ReadRecord property) (ReadRecordV3Columns property)

O

offset (Calibration attribute) (EmbeddedFileData property)

open_file() built-in function OutputHandler (class in pod5.tools.pod5_convert_from_fast5)

P

pack_read_ids() (in module pod5.api_utils) parse_csv_mapping() (in module pod5.tools.pod5_subset) parse_direct_mapping_targets() (in module pod5.tools.pod5_subset) parse_ids() (in module pod5.tools.pod5_filter) parse_json_mapping() (in module pod5.tools.pod5_subset) parse_table_mapping() (in module pod5.tools.pod5_subset) path (Reader property) (Writer property) pending_batch_writes (Repacker property), [1] plan_traversal() (Pod5FileReader method) pod5 module pod5.api_utils module pod5.pod5_types module pod5.reader module pod5.repack module pod5.signal_tools module pod5.tools.pod5_convert_from_fast5 module pod5.tools.pod5_convert_to_fast5 module pod5.tools.pod5_filter module pod5.tools.pod5_inspect module

pod5.tools.pod5_merge module pod5.tools.pod5_repack module pod5.tools.pod5_subset module pod5.tools.pod5_update module pod5.tools.utils module pod5.writer module Pod5ApiException Pod5AsyncSignalLoader (built-in class) Pod5FileReader (built-in class) Pod5RepackerOutput (built-in class) Pod5SignalCacheBatch (built-in class) pore (BaseRead attribute) Pore (class in pod5.pod5_types) pore (ReadRecord property) pore_type (Pore attribute) (ReadRecordV3Columns property) predicted_scaling (BaseRead attribute) (ReadRecord property) predicted_scaling_scale (ReadRecordV3Columns property) predicted_scaling_shift (ReadRecordV3Columns property) print_status() (StatusMonitor method) process_conversion_tasks() (in module pod5.tools.pod5_convert_from_fast5) protocol_name (RunInfo attribute) protocol_run_id (RunInfo attribute) protocol_start_time (RunInfo attribute)

Q

QueueManager (class in pod5.tools.pod5_convert_from_fast5)

R

Read (class in pod5.pod5_types) read_batches() (Reader method) read_id (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) read_id_column (ReadRecordBatch property) read_ids (Reader property) read_ids_raw (Reader property) read_number (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) read_number_column (ReadRecordBatch property) read_table (Reader property) read_table_batch_size (FileWriterOptions attribute) reader (ArrowTableHandle property) Reader (class in pod5.reader) ReadRecord (class in pod5.reader) ReadRecordBatch (class in pod5.reader) ReadRecordV3Columns (class in pod5.reader) reads() (Reader method) (ReadRecordBatch method)

reads_completed (Repacker property), [1] reads_requested (Repacker property) reads_sample_bytes_completed (Repacker property), [1] reads_table_version (Reader property) ReadTableVersion (class in pod5.reader) reason (EndReason attribute) release_next_batch() (Pod5AsyncSignalLoader method) repack_pod5() (in module pod5.tools.pod5_repack) repack_pod5_file() (in module pod5.tools.pod5_repack) Repacker (built-in class) (class in pod5.repack) resolve_one_to_one_path() (OutputHandler static method) resolve_output_path() (OutputHandler static method) resolve_targets() (in module pod5.tools.pod5_subset) run_info (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) run_info_index (ReadRecord property) run_info_table (Reader property) RunInfo (class in pod5.pod5_types) running (StatusMonitor property)

S

safe_close() (in module pod5.api_utils) sample_count (CompressedRead property) (Pod5SignalCacheBatch property) (Read property) (ReadRecord property) (SignalRowInfo property) sample_id (RunInfo attribute) sample_rate (RunInfo attribute) (StatusMonitor property) samples (Pod5SignalCacheBatch property) (Signal property) samples_mb (StatusMonitor property) scale (Calibration attribute) (ShiftScalePair attribute) sequencer_position (RunInfo attribute) sequencer_position_type (RunInfo attribute) sequencing_kit (RunInfo attribute) set_cached_signal() (ReadRecordBatch method) set_input_complete() (OutputHandler method) set_selected_batch_rows() (ReadRecordBatch method) shift (ShiftScalePair attribute) ShiftScalePair (class in pod5.pod5_types) shutdown() (QueueManager method) Signal (class in pod5.reader) signal (Read attribute) (ReadRecord property) (ReadRecordV3Columns property) (Signal property)

signal_batch_row_count (Reader property) signal_chunk_lengths (CompressedRead attribute) signal_chunks (CompressedRead attribute) signal_compression_type (FileWriterOptions attribute) signal_for_chunk() (ReadRecord method) SIGNAL_NEGATIVE (EndReasonEnum attribute) signal_pa (ReadRecord property) SIGNAL_POSITIVE (EndReasonEnum attribute) signal_rows (ReadRecord property) signal_table (Reader property) signal_table_batch_size (FileWriterOptions attribute) SignalRowInfo (class in pod5.reader) software (RunInfo attribute) software_name (Writer property) start (ReadRecordV3Columns property) start_sample (BaseRead attribute) (ReadRecord property) StatusMonitor (class in pod5.tools.pod5_convert_from_fast5) (class in pod5.tools.pod5_convert_to_fast5) subset_pod5() (in module pod5.tools.pod5_subset) subset_pod5s_with_mapping() (in module pod5.tools.pod5_subset) system_name (RunInfo attribute) system_type (RunInfo attribute)

T

terminate_processes() (in module pod5.tools.pod5_convert_from_fast5) time_elapsed (StatusMonitor property) time_since_mux_change (BaseRead attribute) (ReadRecord property) (ReadRecordV3Columns property) timestamp_to_int() (in module pod5.writer) to_read() (ReadRecord method)

total_files (StatusMonitor property) total_reads (StatusMonitor property) tracked_scaling (BaseRead attribute) (ReadRecord property) tracked_scaling_scale (ReadRecordV3Columns property) tracked_scaling_shift (ReadRecordV3Columns property) tracking_id (RunInfo attribute)

U

UNBLOCK_MUX_CHANGE (EndReasonEnum attribute) UNKNOWN (EndReasonEnum attribute)

update_pod5() (in module pod5.tools.pod5_update) update_reads_total() (StatusMonitor method)

V

V3 (ReadTableVersion attribute) vbz_compress_signal() (in module pod5.signal_tools) vbz_compress_signal_chunked() (in module pod5.signal_tools) vbz_compressed_signal_max_size() built-in function

vbz_decompress_signal() (in module pod5.signal_tools) vbz_decompress_signal_chunked() (in module pod5.signal_tools) vbz_decompress_signal_into() (in module pod5.signal_tools)

W

wait() (Repacker method) well (Pore attribute) (ReadRecordV3Columns property)

write() (StatusMonitor method) write_pod5_record_to_fast5() (in module pod5.tools.pod5_convert_to_fast5) Writer (class in pod5.writer) writing_software (Reader property)