Index

A

add_records() (FakeVcfFile method) add_records_from_lines() (FakePlatypusVcfFile method) ALLOWED_TAGS (in module varona.bcftools)

API_DF_SCHEMA (in module varona.platypus) API_LONG_RETRY (in module varona.ensembl) Assembly (class in varona.ensembl)

B

BackportStrEnum (class in varona.enum)

C

CiStrEnum (class in varona.enum)

cli_main() (in module varona.utils.cli_split) close() (VariantFileFilledInTags method)

D

default_vep_cli_json_extractor() (in module varona.extract)

default_vep_response_extractor() (in module varona.extract)

F

FakePlatypusVcfFile (class in varona.fake_vcf)

FakeVcfFile (class in varona.fake_vcf)

H

HAVE_BCFTOOLS (in module varona.bcftools)

HTS_COMPRESSED_VALS (in module varona.ensembl)

I

import_vep_data() (in module varona.ensembl)

M

maf_from_bcftools() (in module varona.maf) maf_from_fr() (in module varona.maf) maf_from_method() (in module varona.maf) maf_from_samples() (in module varona.maf) MafMethod (class in varona.maf) make_header() (FakePlatypusVcfFile method) (FakeVcfFile method) module varona varona.bcftools varona.cli varona.data varona.dataframe varona.ensembl varona.enum varona.extract varona.fake_vcf varona.maf varona.platypus varona.utils varona.utils.cli_split varona.utils.fix_vcf varona.utils.misc varona.utils.split

multi_suffix_stem() (in module varona.utils.misc)

P

parse_args() (VaronaArgumentParser method)

platypus_dataframe() (in module varona.platypus) platypus_vcf_record_extractor() (in module varona.extract)

Q

query_vep_api() (in module varona.ensembl)

R

run_bcftools_fill_tags() (in module varona.bcftools)

S

setUp() (TestWithTempDir method)

split_vcf() (in module varona.utils.split)

T

tearDown() (TestWithTempDir method)

TestWithTempDir (class in varona.fake_vcf)

V

VariantFileFilledInTags (class in varona.bcftools) varona module varona.bcftools module varona.cli module varona.data module varona.dataframe module varona.ensembl module varona.enum module varona.extract module varona.fake_vcf module varona.maf module

varona.platypus module varona.utils module varona.utils.cli_split module varona.utils.fix_vcf module varona.utils.misc module varona.utils.split module VaronaArgumentParser (class in varona.cli) vcf_dataframe() (in module varona.dataframe) VCF_DF_SCHEMA (in module varona.platypus) vcf_header_inject_contigs() (in module varona.utils.fix_vcf) VCF_MASK_COLS (in module varona.ensembl) vcf_rows() (in module varona.ensembl) vcf_split_args() (in module varona.utils.cli_split) vcf_to_vep_query_data() (in module varona.ensembl) vep_api_dataframe() (in module varona.dataframe)

W

write_vcf() (FakePlatypusVcfFile method) (FakeVcfFile method)