Index

_

_Condition (class in readfish._config)

_PluginModule (class in readfish._config)

A

above_max_chunks (readfish.plugins.utils.Decision attribute) Action (class in readfish.plugins.utils) actions (readfish._statistics.ReadfishStatistics attribute) actions_conditions (readfish._statistics.ReadfishStatistics attribute) add_action() (readfish.plugins.utils.PreviouslySentActionTracker method) add_batch_performance() (readfish._statistics.ReadfishStatistics method)

Aligner (class in readfish.plugins._no_op) AlignerABC (class in readfish.plugins.abc) alignment_data (readfish.plugins.utils.Result attribute) average_batch_size (readfish._statistics.ReadfishStatistics property) average_batch_time (readfish._statistics.ReadfishStatistics property) average_chunks_per_second (readfish._statistics.ReadfishStatistics property)

B

Barcode (class in readfish._config) barcode (readfish.plugins.utils.Result attribute) basecall() (readfish.plugins._no_op.Caller method) (readfish.plugins.abc.CallerABC method) (readfish.plugins.dorado.Caller method)

basecall_data (readfish.plugins.utils.Result attribute) batch_statistics (readfish._statistics.ReadfishStatistics attribute) below_min_chunks (readfish.plugins.utils.Decision attribute) break_reads_seconds (readfish._statistics.ReadfishStatistics attribute)

C

Caller (class in readfish.plugins._no_op) (class in readfish.plugins.dorado) CallerABC (class in readfish.plugins.abc) CallerSettings (class in readfish._config) channel (readfish.plugins.utils.Result attribute) check_coord() (readfish.plugins.utils.Targets method)

Chemistry (class in readfish._cli_args) ChunkTracker (class in readfish._utils) compress_and_encode_string() (in module readfish._utils) conditions (readfish._statistics.ReadfishStatistics attribute) Conf (class in readfish._config) coord_validator() (in module readfish.plugins.utils) count_dict_elements() (in module readfish.plugins.utils)

D

debug_logger (readfish._statistics.ReadfishStatistics attribute) Decision (class in readfish.plugins.utils) decision (readfish.plugins.utils.Result attribute) decisions (readfish._statistics.ReadfishStatistics attribute) decode_and_decompress_string() (in module readfish._utils) describe() (readfish.plugins._no_op.Aligner method) (readfish.plugins._no_op.Caller method) (readfish.plugins.abc.AlignerABC method) (readfish.plugins.abc.CallerABC method) (readfish.plugins.dorado.Caller method)

describe_experiment() (readfish._config.Conf method) disconnect() (readfish.plugins._no_op.Aligner method) (readfish.plugins._no_op.Caller method) (readfish.plugins.abc.AlignerABC method) (readfish.plugins.abc.CallerABC method) (readfish.plugins.dorado.Caller method) draw_flowcell_split() (in module readfish._utils) DUPLEX (readfish._cli_args.Chemistry attribute) duplex_override (readfish.plugins.utils.Decision attribute) DUPLEX_SIMPLE (readfish._cli_args.Chemistry attribute) DuplexTracker (class in readfish.plugins.utils)

E

ERROR (readfish._utils.Severity attribute)

escape_message_to_minknow() (in module readfish._utils)

F

first_read_override (readfish.plugins.utils.Decision attribute) first_read_overrides (readfish._statistics.ReadfishStatistics attribute) format_bases() (in module readfish._utils) forward (readfish.plugins.utils.Strand attribute)

from_dict() (readfish._config._PluginModule class method) (readfish._config.Conf class method) from_file() (readfish._config.Conf class method) from_parsed_toml() (readfish.plugins.utils.Targets class method)

G

generate_flowcell() (in module readfish._utils) get_action() (readfish._config._Condition method) (readfish.plugins.utils.PreviouslySentActionTracker method) get_barcode() (readfish._config.Conf method) get_batch_performance() (readfish._statistics.ReadfishStatistics method) get_conditions() (readfish._config.Conf method) get_contig_lengths() (in module readfish.plugins.utils)

get_coords() (in module readfish._utils) get_device() (in module readfish._utils) get_flowcell_array() (in module readfish._utils) get_offset() (readfish.plugins.utils.Targets method) get_previous_alignments() (readfish.plugins.utils.DuplexTracker method) get_previous_decision() (readfish.plugins.utils.DuplexTracker method) get_region() (readfish._config.Conf method) get_targets() (readfish._config.Conf method)

I

INFO (readfish._utils.Severity attribute) initialised (readfish.plugins.abc.AlignerABC property) initialised() (readfish.plugins._no_op.Aligner method)

is_empty() (in module readfish.plugins.utils) iter_exception_group() (in module readfish._utils) iter_targets() (readfish.plugins.utils.Targets method)

L

last_actions (readfish.plugins.utils.PreviouslySentActionTracker attribute) load_module() (readfish._config._PluginModule method)

load_object() (readfish._config._PluginModule method) log_file (readfish._statistics.ReadfishStatistics attribute) log_read() (readfish._statistics.ReadfishStatistics method)

M

main() (in module readfish._cli_base) map_reads() (readfish.plugins._no_op.Aligner method) (readfish.plugins.abc.AlignerABC method) MapperSettings (class in readfish._config) module readfish._cli_args readfish._cli_base readfish._config readfish._loggers readfish._statistics readfish._utils readfish.entry_points.stats readfish.entry_points.targets readfish.entry_points.unblock_all readfish.entry_points.validate readfish.plugins._no_op readfish.plugins.abc readfish.plugins.dorado readfish.plugins.mappy readfish.plugins.utils

multi_off (readfish.plugins.utils.Decision attribute) multi_on (readfish.plugins.utils.Decision attribute)

N

nested_get() (in module readfish._utils) nice_join() (in module readfish._utils)

no_map (readfish.plugins.utils.Decision attribute) no_seq (readfish.plugins.utils.Decision attribute)

P

padding (readfish.plugins.utils.Targets attribute) possible_duplex() (readfish.plugins.utils.DuplexTracker method) pretty_print() (readfish._config._Condition method) previous_alignments (readfish.plugins.utils.DuplexTracker attribute)

previous_decision (readfish.plugins.utils.DuplexTracker attribute) PreviouslySentActionTracker (class in readfish.plugins.utils) print_args() (in module readfish._loggers) proceed (readfish.plugins.utils.Action attribute)

R

read_id (readfish.plugins.utils.Result attribute) readfish._cli_args module readfish._cli_base module readfish._config module readfish._loggers module readfish._statistics module readfish._utils module readfish.entry_points.stats module readfish.entry_points.targets module readfish.entry_points.unblock_all module

readfish.entry_points.validate module readfish.plugins._no_op module readfish.plugins.abc module readfish.plugins.dorado module readfish.plugins.mappy module readfish.plugins.utils module ReadfishStatistics (class in readfish._statistics) Region (class in readfish._config) Result (class in readfish.plugins.utils) reverse (readfish.plugins.utils.Strand attribute) row_checker() (in module readfish.plugins.utils)

S

seen() (readfish._utils.ChunkTracker method) send_message() (in module readfish._utils) seq (readfish.plugins.utils.Result attribute) set_alignments() (readfish.plugins.utils.DuplexTracker method) set_decision() (readfish.plugins.utils.DuplexTracker method) setup_logger() (in module readfish._loggers) Severity (class in readfish._utils)

SIMPLEX (readfish._cli_args.Chemistry attribute) single_off (readfish.plugins.utils.Decision attribute) single_on (readfish.plugins.utils.Decision attribute) stop_receiving (readfish.plugins.utils.Action attribute) Strand (class in readfish.plugins.utils) strand_validator() (in module readfish.plugins.utils) stringify_grid() (in module readfish._utils) sum_target_coverage() (in module readfish.plugins.utils)

T

TARGET_INTERVAL (in module readfish.plugins.utils) Targets (class in readfish.plugins.utils)

to_file() (readfish._config.Conf method) total_chunks (readfish._statistics.ReadfishStatistics attribute)

U

unblock (readfish.plugins.utils.Action attribute)

V

validate() (readfish.plugins._no_op.Aligner method) (readfish.plugins._no_op.Caller method) (readfish.plugins.abc.AlignerABC method) (readfish.plugins.abc.CallerABC method) (readfish.plugins.dorado.Caller method)

value (readfish.plugins.utils.Targets attribute)

W

WARN (readfish._utils.Severity attribute)

write_channels_toml() (readfish._config.Conf method)