Index

A

annotate_vcf() (in module strvcf_annotator.api) annotate_vcf_file() (strvcf_annotator.api.STRAnnotator method)

annotate_vcf_stream() (strvcf_annotator.api.STRAnnotator method) annotate_vcf_to_file() (in module strvcf_annotator.core.vcf_processor) apply_variant_to_repeat() (in module strvcf_annotator.core.repeat_utils)

B

BaseVCFParser (class in strvcf_annotator.parsers.base)

build_new_record() (in module strvcf_annotator.core.annotation)

C

check_vcf_sorted() (in module strvcf_annotator.core.vcf_processor)

chrom_to_order() (in module strvcf_annotator.utils.vcf_utils) count_repeat_units() (in module strvcf_annotator.core.repeat_utils)

E

extract_info() (strvcf_annotator.parsers.base.BaseVCFParser method) (strvcf_annotator.parsers.generic.GenericParser method)

extract_repeat_sequence() (in module strvcf_annotator.core.repeat_utils)

F

find_overlapping_str() (in module strvcf_annotator.core.str_reference)

G

generate_annotated_records() (in module strvcf_annotator.core.vcf_processor) GenericParser (class in strvcf_annotator.parsers.generic) get_genotype() (strvcf_annotator.parsers.base.BaseVCFParser method) (strvcf_annotator.parsers.generic.GenericParser method)

get_sample_by_index() (in module strvcf_annotator.utils.vcf_utils) get_sample_by_name() (in module strvcf_annotator.utils.vcf_utils) get_statistics() (strvcf_annotator.api.STRAnnotator method) get_str_at_position() (in module strvcf_annotator.core.str_reference) (strvcf_annotator.api.STRAnnotator method)

H

has_format_field() (in module strvcf_annotator.utils.vcf_utils)

has_variant() (strvcf_annotator.parsers.base.BaseVCFParser method) (strvcf_annotator.parsers.generic.GenericParser method)

I

is_perfect_repeat() (in module strvcf_annotator.core.repeat_utils)

L

load_str_reference() (in module strvcf_annotator.core.str_reference)

M

make_modified_header() (in module strvcf_annotator.core.annotation) module strvcf_annotator.api strvcf_annotator.core.annotation strvcf_annotator.core.repeat_utils strvcf_annotator.core.str_reference strvcf_annotator.core.vcf_processor strvcf_annotator.parsers.base strvcf_annotator.parsers.generic strvcf_annotator.utils.validation strvcf_annotator.utils.vcf_utils

N

normalize_info_fields() (in module strvcf_annotator.utils.vcf_utils)

normalize_variant() (in module strvcf_annotator.core.repeat_utils)

P

parser (strvcf_annotator.api.STRAnnotator attribute)

process_directory() (in module strvcf_annotator.core.vcf_processor) (strvcf_annotator.api.STRAnnotator method)

R

reset_and_sort_vcf() (in module strvcf_annotator.core.vcf_processor)

S

should_skip_genotype() (in module strvcf_annotator.core.annotation) somatic_mode (strvcf_annotator.api.STRAnnotator attribute) str_bed_path (strvcf_annotator.api.STRAnnotator attribute) str_df (strvcf_annotator.api.STRAnnotator attribute) STRAnnotator (class in strvcf_annotator.api) strvcf_annotator.api module strvcf_annotator.core.annotation module strvcf_annotator.core.repeat_utils module

strvcf_annotator.core.str_reference module strvcf_annotator.core.vcf_processor module strvcf_annotator.parsers.base module strvcf_annotator.parsers.generic module strvcf_annotator.utils.validation module strvcf_annotator.utils.vcf_utils module

V

validate_bed_file() (in module strvcf_annotator.utils.validation) validate_directory_path() (in module strvcf_annotator.utils.validation) validate_file_path() (in module strvcf_annotator.utils.validation) validate_record() (strvcf_annotator.parsers.base.BaseVCFParser method) (strvcf_annotator.parsers.generic.GenericParser method)

validate_str_bed_file() (in module strvcf_annotator.utils.validation) validate_vcf_file() (in module strvcf_annotator.utils.validation) ValidationError