Index

A

allele_freq_annos() (truvari.VariantRecord method)

B

bed_ranges() (in module truvari) Bench (class in truvari) benchdir_count_entries() (in module truvari) BenchOutput (class in truvari) best_seqsim() (in module truvari)

bnd_direction_strand() (truvari.VariantRecord method) bnd_match() (truvari.VariantRecord method) bnd_position() (truvari.VariantRecord method) boundaries() (truvari.VariantRecord method) build_matrix() (truvari.Bench method) build_region_tree() (in module truvari)

C

calc_performance() (truvari.StatsBox method) calc_score() (truvari.MatchResult method) check_refine_candidate() (truvari.Bench method) check_vcf_index() (in module truvari) chunker() (in module truvari) close_outputs() (truvari.BenchOutput method) cmd_exe() (in module truvari)

compare_calls() (truvari.Bench method) compare_chunk() (truvari.Bench method) compare_gts() (truvari.VariantRecord method) compress_index_vcf() (in module truvari) coords_within() (in module truvari) copy() (truvari.VariantRecord method) count_entries() (in module truvari) cpx_match() (truvari.VariantRecord method)

D

decompose() (truvari.VariantRecord method)

distance() (truvari.VariantRecord method)

E

extend_region_tree() (in module truvari)

F

fetch() (truvari.VariantFile method) fetch_bed() (truvari.VariantFile method) fetch_regions() (truvari.VariantFile method)

file_zipper() (in module truvari) filter_call() (truvari.VariantRecord method) filter_size() (truvari.VariantRecord method) flush() (truvari.LogFileStderr method)

G

get_alt() (truvari.VariantRecord method) get_gt() (in module truvari) get_record() (truvari.VariantRecord method) get_ref() (truvari.VariantRecord method)

get_scalebin() (in module truvari) get_sizebin() (in module truvari) get_svtype() (in module truvari) GT (class in truvari) gt() (truvari.VariantRecord method)

H

HEADERMAT (in module truvari)

help_unknown_cmd() (in module truvari)

I

is_bnd() (truvari.VariantRecord method) is_filtered() (truvari.VariantRecord method) is_monrefstar() (truvari.VariantRecord method) is_multi() (truvari.VariantRecord method)

is_present() (truvari.VariantRecord method) is_resolved() (truvari.VariantRecord method) is_single_bnd() (truvari.VariantRecord method) is_symbolic() (truvari.VariantRecord method)

L

LogFileStderr (class in truvari)

M

make_temp_filename() (in module truvari) match() (truvari.VariantRecord method) MatchResult (class in truvari) merge_region_tree_overlaps() (in module truvari)

module truvari move_record() (truvari.VariantRecord method) msa2vcf() (in module truvari)

O

opt_gz_open() (in module truvari) optimize_df_memory() (in module truvari)

overlap_percent() (in module truvari) overlaps() (in module truvari)

P

param_dict() (truvari.Bench method)

performance_metrics() (in module truvari) phab() (in module truvari)

Q

QUALBINS (in module truvari)

R

read_bed_tree() (in module truvari) reciprocal_overlap() (in module truvari) recovl() (truvari.VariantRecord method) ref_ranges() (in module truvari)

resolve() (truvari.VariantRecord method) restricted_float() (in module truvari) restricted_int() (in module truvari) roll_seqsim() (in module truvari) run() (truvari.Bench method)

S

same_type() (truvari.VariantRecord method) seqsim() (in module truvari) (truvari.VariantRecord method) setup_logging() (in module truvari) sizesim() (in module truvari) (truvari.VariantRecord method)

StatsBox (class in truvari) SV (class in truvari) SZBINMAX (in module truvari) SZBINS (in module truvari)

T

to_hash() (truvari.VariantRecord method) to_key() (truvari.VariantRecord method)

truvari module

U

unroll_seqsim() (in module truvari)

V

var_match() (truvari.VariantRecord method) var_size() (truvari.VariantRecord method) var_type() (truvari.VariantRecord method) VariantFile (class in truvari)

VariantParams (class in truvari) VariantRecord (class in truvari) vcf_ranges() (in module truvari) vcf_to_df() (in module truvari)

W

within() (truvari.VariantRecord method) within_tree() (truvari.VariantRecord method) write() (truvari.LogFileStderr method) (truvari.VariantFile method)

write_json() (truvari.StatsBox method) write_match() (truvari.BenchOutput method)