Index

A

active_mux() (fast5_research.fast5_bulk.AsicBConfiguration method) argmax() (fast5_research.util.MockZeroArray method) AsicBCommand (class in fast5_research.fast5_bulk)

AsicBConfiguration (class in fast5_research.fast5_bulk) assert_writable() (fast5_research.fast5.Fast5 method) attributes() (fast5_research.fast5.Fast5 property)

B

bias_voltage() (fast5_research.fast5_bulk.AsicBConfiguration property) bits_at() (fast5_research.fast5_bulk.AsicBConfiguration method) build_mapping_summary_table() (in module fast5_research.util)

build_mapping_table() (in module fast5_research.util) build_read_index() (in module fast5_research.extract) BulkFast5 (class in fast5_research.fast5_bulk)

C

channel_meta() (fast5_research.fast5.Fast5 property) close() (fast5_research.extract.MultiWriter method) compute_movement_stats() (in module fast5_research.util) configuration() (fast5_research.fast5_bulk.AsicBCommand property) context_tags() (fast5_research.fast5.Fast5 property)

convert_channel_id() (fast5_research.fast5.Fast5 static method) convert_raw_meta() (fast5_research.fast5.Fast5 static method) convert_tracking_id() (fast5_research.fast5.Fast5 static method) create_basecall_1d_output() (in module fast5_research.util) create_mapping_output() (in module fast5_research.util)

D

docstring_parameter() (in module fast5_research.util)

dtype_descr() (in module fast5_research.util)

E

extract_channel_reads() (in module fast5_research.extract) extract_read_summary() (in module fast5_research.extract)

extract_read_summary_internal() (in module fast5_research.extract) extract_reads() (in module fast5_research.extract)

F

Fast5 (class in fast5_research.fast5) fast5_research module fast5_research.extract module fast5_research.fast5 module

fast5_research.fast5_bulk module fast5_research.util module file_has_fields() (in module fast5_research.util) filter_file_from_bam() (in module fast5_research.extract) filter_multi_reads() (in module fast5_research.extract)

G

get_alignment_attrs() (fast5_research.fast5.Fast5 method) get_analysis_latest() (fast5_research.fast5.Fast5 method) get_analysis_new() (fast5_research.fast5.Fast5 method) get_any_mapping_data() (fast5_research.fast5.Fast5 method) get_basecall_data() (fast5_research.fast5.Fast5 method) get_bias_voltage_changes() (fast5_research.fast5_bulk.BulkFast5 method) get_bias_voltage_changes_in_window() (fast5_research.fast5_bulk.BulkFast5 method) get_changes() (in module fast5_research.util) get_context_meta() (fast5_research.fast5_bulk.BulkFast5 method) get_engine_state() (fast5_research.fast5.Fast5 method) (fast5_research.fast5_bulk.BulkFast5 method) get_event_detection_parameters() (fast5_research.fast5_bulk.BulkFast5 method) get_events() (fast5_research.fast5_bulk.BulkFast5 method) get_fastq() (fast5_research.fast5.Fast5 method) get_mapping_attrs() (fast5_research.fast5.Fast5 method) get_mapping_data() (fast5_research.fast5.Fast5 method) get_metadata() (fast5_research.fast5_bulk.BulkFast5 method) get_model() (fast5_research.fast5.Fast5 method) get_mux() (fast5_research.fast5_bulk.BulkFast5 method) get_mux_changes() (fast5_research.fast5_bulk.BulkFast5 method)

get_mux_changes_in_window() (fast5_research.fast5_bulk.BulkFast5 method) get_raw() (fast5_research.fast5.Fast5 method) (fast5_research.fast5_bulk.BulkFast5 method) get_read() (fast5_research.fast5.Fast5 method) get_read_stats() (fast5_research.fast5.Fast5 method) get_reads() (fast5_research.fast5.Fast5 method) (fast5_research.fast5_bulk.BulkFast5 method) get_reference_fasta() (fast5_research.fast5.Fast5 method) get_sam() (fast5_research.fast5.Fast5 method) get_section_events() (fast5_research.fast5.Fast5 method) get_section_indices() (fast5_research.fast5.Fast5 method) get_split_data() (fast5_research.fast5.Fast5 method) get_state() (fast5_research.fast5_bulk.BulkFast5 method) get_state_changes() (fast5_research.fast5_bulk.BulkFast5 method) get_states_in_window() (fast5_research.fast5_bulk.BulkFast5 method) get_temperature() (fast5_research.fast5.Fast5 method) (fast5_research.fast5_bulk.BulkFast5 method) get_tracking_meta() (fast5_research.fast5_bulk.BulkFast5 method) get_voltage() (fast5_research.fast5_bulk.BulkFast5 method) get_waveform_timings() (fast5_research.fast5_bulk.BulkFast5 method) group_vector() (in module fast5_research.util)

H

has_raw() (fast5_research.fast5_bulk.BulkFast5 method)

has_reads() (fast5_research.fast5_bulk.BulkFast5 method) has_states() (fast5_research.fast5_bulk.BulkFast5 method)

I

int_at() (fast5_research.fast5_bulk.AsicBConfiguration method)

iterate_fast5() (in module fast5_research.fast5)

K

kmer_overlap_gen() (in module fast5_research.util)

M

mad() (in module fast5_research.util) mean_qscore() (in module fast5_research.util) med_mad() (in module fast5_research.util) min_temperature() (fast5_research.fast5_bulk.AsicBCommand property) MockZeroArray (class in fast5_research.util) module fast5_research fast5_research.extract fast5_research.fast5 fast5_research.fast5_bulk fast5_research.util

MultiWriter (class in fast5_research.extract)

N

New() (fast5_research.fast5.Fast5 class method) (fast5_research.fast5_bulk.BulkFast5 class method)

P

parse_history() (fast5_research.fast5_bulk.BulkFast5 method)

Q

qstring_to_phred() (in module fast5_research.util)

R

Read (class in fast5_research.extract) reads_in_multi() (in module fast5_research.extract) readtsv() (in module fast5_research.util)

ReadWriter (class in fast5_research.extract) recursive_glob() (in module fast5_research.fast5) repack() (fast5_research.fast5.Fast5 method)

S

seq_to_kmers() (in module fast5_research.util) set_basecall_data() (fast5_research.fast5.Fast5 method) set_engine_state() (fast5_research.fast5.Fast5 method) set_events() (fast5_research.fast5_bulk.BulkFast5 method) set_mapping_data() (fast5_research.fast5.Fast5 method) set_raw() (fast5_research.fast5.Fast5 method) (fast5_research.fast5_bulk.BulkFast5 method)

set_raw_old() (fast5_research.fast5.Fast5 method) set_read() (fast5_research.fast5.Fast5 method) set_split_data() (fast5_research.fast5.Fast5 method) set_voltage() (fast5_research.fast5_bulk.BulkFast5 method) SingleWriter (class in fast5_research.extract) strip_analyses() (fast5_research.fast5.Fast5 method) summary() (fast5_research.fast5.Fast5 method)

T

time_cast() (in module fast5_research.extract)

tracking_id() (fast5_research.fast5.Fast5 property) triplewise() (in module fast5_research.extract)

V

validate_event_table() (in module fast5_research.util)

validate_model_table() (in module fast5_research.util) validate_scale_object() (in module fast5_research.util)

W

window() (in module fast5_research.util) writable() (fast5_research.fast5.Fast5 property)

write_read() (fast5_research.extract.MultiWriter method) (fast5_research.extract.ReadWriter method) (fast5_research.extract.SingleWriter method)