VAPr
latest
Contents:
Introduction
Downstream Analysis
VAPr core
Tutorial
API Reference
VAPr
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
_
_raw_string (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
A
Allele (class in VAPr.vcf_genotype_fields_parsing)
allele1_number (VAPr.vcf_genotype_fields_parsing.GenotypeLikelihood attribute)
allele2_number (VAPr.vcf_genotype_fields_parsing.GenotypeLikelihood attribute)
ALLELE_DEPTH_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
alleles (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
ALT_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
annotate() (VAPr.vapr_core.VaprAnnotator method)
annotate_lite() (VAPr.vapr_core.VaprAnnotator method)
AnnotationJobParamsIndices (class in VAPr.chunk_processing)
ANNOVAR_ANNOTATION_CONTENT (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser attribute)
AnnovarAnnotatedVariant (class in VAPr.annovar_output_parsing)
AnnovarTxtParser (class in VAPr.annovar_output_parsing)
AnnovarWrapper (class in VAPr.annovar_running)
B
bgzip_and_index_vcf() (in module VAPr.vcf_merging)
C
CHR_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
CHUNK_INDEX_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
CHUNK_SIZE_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
collect_chunk_annotations_and_store() (in module VAPr.chunk_processing)
COLLECTION_NAME_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
convert_to_nonneg_int() (in module VAPr.validation)
convert_to_nullable() (in module VAPr.validation)
CYTOBAND_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
D
DB_NAME_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
DEFAULT_GENOME_VERSION (VAPr.vapr_core.VaprAnnotator attribute)
download_annovar_databases() (VAPr.vapr_core.VaprAnnotator method)
download_databases() (VAPr.annovar_running.AnnovarWrapper method)
E
END_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
ESP6500_ALL_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
EXONICFUNC_KNOWNGENE_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
F
FILE_PATH_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
filter_passing_reads_count (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
FILTER_PASSING_READS_COUNT_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
FILTERED_ALLELE_DEPTH_TAG (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser attribute)
full_name (VAPr.vapr_core.VaprDataset attribute)
FUNC_KNOWNGENE_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
G
GENE_KNOWNGENE_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
GENEDETAIL_KNOWNGENE_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
GENOME_BUILD_VERSION_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
GENOMIC_SUPERDUPS_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
genotype (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
genotype_confidence (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
GENOTYPE_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
genotype_likelihoods (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
GENOTYPE_LIKELIHOODS_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
GENOTYPE_QUALITY_TAG (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser attribute)
genotype_subclass_by_class (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
GENOTYPE_SUBCLASS_BY_CLASS_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
GENOTYPE_TAG (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser attribute)
GenotypeLikelihood (class in VAPr.vcf_genotype_fields_parsing)
get_all_variants() (VAPr.vapr_core.VaprDataset method)
get_any_of_sample_ids_filter() (in module VAPr.filtering)
get_custom_filtered_variants() (VAPr.vapr_core.VaprDataset method)
get_de_novo_variants() (VAPr.vapr_core.VaprDataset method)
get_deleterious_compound_heterozygous_variants() (VAPr.vapr_core.VaprDataset method)
get_distinct_sample_ids() (VAPr.vapr_core.VaprDataset method)
get_known_disease_variants() (VAPr.vapr_core.VaprDataset method)
get_num_possible_indices() (VAPr.chunk_processing.AnnotationJobParamsIndices class method)
get_rare_deleterious_variants() (VAPr.vapr_core.VaprDataset method)
get_sample_id_filter() (in module VAPr.filtering)
get_variants_as_dataframe() (VAPr.vapr_core.VaprDataset method)
get_variants_for_sample() (VAPr.vapr_core.VaprDataset method)
get_variants_for_samples() (VAPr.vapr_core.VaprDataset method)
H
help_get_test_file_info() (in module VAPr.tests.test_vcf_merging)
help_make_filter() (in module VAPr.tests.test_vapr_core)
HG00096_VCF_CONTENTS (VAPr.tests.test_vcf_merging.TestFunctions attribute)
HG00097_VCF_CONTENTS (VAPr.tests.test_vcf_merging.TestFunctions attribute)
HG19_VERSION (VAPr.vapr_core.VaprAnnotator attribute)
HG38_VERSION (VAPr.vapr_core.VaprAnnotator attribute)
hg_19_databases (VAPr.annovar_running.AnnovarWrapper attribute)
hg_38_databases (VAPr.annovar_running.AnnovarWrapper attribute)
HGVS_ID_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
I
is_empty (VAPr.vapr_core.VaprDataset attribute)
is_valid_genotype_fields_string() (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser static method)
L
likelihood_neg_exponent (VAPr.vcf_genotype_fields_parsing.GenotypeLikelihood attribute)
M
make_de_novo_variants_filter() (in module VAPr.filtering)
make_deleterious_compound_heterozygous_variants_filter() (in module VAPr.filtering)
make_known_disease_variants_filter() (in module VAPr.filtering)
make_per_variant_annotation_dict() (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant class method)
make_rare_deleterious_variants_filter() (in module VAPr.filtering)
merge_vcfs() (in module VAPr.vcf_merging)
N
NCI60_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
NORMALIZED_SCALED_LIKELIHOODS_TAG (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser attribute)
num_records (VAPr.vapr_core.VaprDataset attribute)
O
OTHERINFO_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
P
parse() (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser class method)
R
RAW_CHR_MT_SUFFIX_VAL (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
RAW_CHR_MT_VAL (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
read_chunk_of_annotations_to_dicts_list() (VAPr.annovar_output_parsing.AnnovarTxtParser class method)
REF_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
run_annotation() (VAPr.annovar_running.AnnovarWrapper method)
S
SAMPLE_ID_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
SAMPLE_LIST_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
SAMPLE_NAMES_KEY (VAPr.vapr_core.VaprAnnotator attribute)
SAMPLES_KEY (VAPr.annovar_output_parsing.AnnovarAnnotatedVariant attribute)
SCORE_KEY (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
setUpClass() (VAPr.tests.test_annovar_running.TestAnnovarWrapper class method)
(VAPr.tests.test_vapr_core.TestVaprDataset class method)
(VAPr.tests.test_vcf_merging.TestFunctions class method)
STANDARDIZED_CHR_MT_SUFFIX_VAL (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
STANDARDIZED_CHR_MT_VAL (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
START_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
SUPPORTED_GENOME_BUILD_VERSIONS (VAPr.vapr_core.VaprAnnotator attribute)
T
test___init__single_bzipped_file() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__append_sample_id_constraint_if_needed_is_needed() (VAPr.tests.test_filtering.TestFunctions method)
test__append_sample_id_constraint_if_needed_is_not_needed() (VAPr.tests.test_filtering.TestFunctions method)
test__build_annovar_database_download_command_str() (VAPr.tests.test_annovar_running.TestAnnovarWrapper method)
test__build_bgzip_vcf_command_str() (VAPr.tests.test_vcf_merging.TestFunctions method)
test__build_index_vcf_command_str() (VAPr.tests.test_vcf_merging.TestFunctions method)
test__build_merge_vcf_command_str() (VAPr.tests.test_vcf_merging.TestFunctions method)
test__build_table_annovar_command_str() (VAPr.tests.test_annovar_running.TestAnnovarWrapper method)
test__collect_chunk_annotations_no_sample_info() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__collect_chunk_annotations_with_sample_info() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__get_annovar_dbs_to_use_for_build_version_error() (VAPr.tests.test_annovar_running.TestAnnovarWrapper method)
test__get_annovar_dbs_to_use_for_build_version_hg19() (VAPr.tests.test_annovar_running.TestAnnovarWrapper method)
test__get_annovar_dbs_to_use_for_build_version_hg38() (VAPr.tests.test_annovar_running.TestAnnovarWrapper method)
test__get_filtered_variants_by_sample_all() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test__get_filtered_variants_by_sample_single() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test__get_filtered_variants_by_sample_some() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test__get_hgvs_ids_from_vcf() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__get_myvariantinfo_annotations_dict() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__get_myvariantinfo_annotations_dict_fatal_error_immediately() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__get_num_lines_in_file() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__get_validated_genome_version() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__get_validated_genome_version_default() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__get_validated_genome_version_error() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__get_vcf_file_paths_list_in_directory() (VAPr.tests.test_vcf_merging.TestFunctions method)
test__get_vcf_file_paths_list_in_directory_none() (VAPr.tests.test_vcf_merging.TestFunctions method)
test__list_has_valid_content_false_all_none() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test__list_has_valid_content_false_empty() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test__list_has_valid_content_true() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test__make_jobs_params_tuples_list_no_samples_default_verbose() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__make_jobs_params_tuples_list_no_samples_default_verbose_less_than_chunk() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__make_jobs_params_tuples_list_samples_with_verbose() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__make_merged_vcf_w_design_file() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__make_merged_vcf_wo_design_file() (VAPr.tests.test_vapr_core.TestVaprAnnotator method)
test__make_per_sample_annotation_dict_maximum_content() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test__make_per_sample_annotation_dict_minimum_content() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test__make_per_sample_annotation_dict_none() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test__merge_annovar_and_myvariant_dicts() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__merge_annovar_and_myvariant_dicts_error() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__merge_bgzipped_indexed_vcfs() (VAPr.tests.test_vcf_merging.TestFunctions method)
test__normalize_header() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__parse_single_variant_record() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__parse_to_dict_with_score_key() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__remove_unwanted_keys() (VAPr.tests.test_chunk_processing.TestFunctions method)
test__rewrite_value_if_special_header_chrom_cleaned() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__rewrite_value_if_special_header_chrom_unchanged() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__rewrite_value_if_special_header_to_dict_w_score() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__rewrite_value_if_special_header_to_float() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__rewrite_value_if_special_header_to_int() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__rewrite_value_if_special_header_unchanged() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test__validate_allele_relationship_fail() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test__validate_allele_relationship_pass() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test__warn_if_no_output_false() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test__warn_if_no_output_true() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test__write_annotated_csv() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test__write_annotated_vcf() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_allele1_number_setter() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test_allele1_number_setter_error() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test_allele2_number_setter() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test_allele2_number_setter_error() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test_bgzip_and_index_vcf_is_vcf_gz() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_bgzip_and_index_vcf_not_vcf_gz() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_convert_to_nonneg_int_fail_negative() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nonneg_int_fail_negative_non_integer() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nonneg_int_not_integer() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nonneg_int_not_nullable_pass() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nonneg_int_nullable_fail() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nonneg_int_nullable_pass_null() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nullable_not_null() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nullable_not_null_error() (VAPr.tests.test_validation.TestFunctions method)
test_convert_to_nullable_null() (VAPr.tests.test_validation.TestFunctions method)
test_de_novo_variants() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_deleterious_compound_heterozygous_variants_all_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_deleterious_compound_heterozygous_variants_specific_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_fill_filtered_reads_count() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_confidence() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_likelihoods_no_alleles() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_likelihoods_three_alleles() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_likelihoods_warn_too_few_likelihoods_1() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_likelihoods_warn_too_few_likelihoods_2() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_likelihoods_warn_too_many_alleles_implied() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_genotype_warn() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_unfiltered_reads_counts() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_fill_unfiltered_reads_counts_warn() (VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions method)
test_filter_passing_reads_count_setter() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeInfo method)
test_filter_passing_reads_count_setter_error() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeInfo method)
test_genotype_confidence_setter() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeInfo method)
test_genotype_confidence_setter_error() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
(VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeInfo method)
test_get_all_variants() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_any_of_sample_ids_filter() (VAPr.tests.test_filtering.TestFunctions method)
test_get_custom_filtered_variants() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_custom_filtered_variants_empty_db() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_distinct_sample_ids() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_num_possible_indices() (VAPr.tests.test_chunk_processing.TestAnnotationJobParamsIndices method)
test_get_sample_id_filter() (VAPr.tests.test_filtering.TestFunctions method)
test_get_variants_as_dataframe_all() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_variants_as_dataframe_some() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_variants_for_sample() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_get_variants_for_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_is_valid_genotype_fields_string_false_delimited() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString method)
test_is_valid_genotype_fields_string_false_period() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString method)
test_is_valid_genotype_fields_string_true() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString method)
test_known_disease_variants_all_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_known_disease_variants_specific_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_likelihood_neg_exponent_setter() (VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood method)
test_make_de_novo_variants_filter() (VAPr.tests.test_filtering.TestFunctions method)
test_make_deleterious_compound_heterozygote_variants_filter_w_samples() (VAPr.tests.test_filtering.TestFunctions method)
test_make_deleterious_compound_heterozygote_variants_filter_wo_samples() (VAPr.tests.test_filtering.TestFunctions method)
test_make_known_disease_variants_filter_w_samples() (VAPr.tests.test_filtering.TestFunctions method)
test_make_known_disease_variants_filter_wo_samples() (VAPr.tests.test_filtering.TestFunctions method)
test_make_per_variant_annotation_dict() (VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant method)
test_make_rare_deleterious_variants_filter_w_samples() (VAPr.tests.test_filtering.TestFunctions method)
test_make_rare_deleterious_variants_filter_wo_samples() (VAPr.tests.test_filtering.TestFunctions method)
test_merge_vcfs_by_dir_error_no_files_found_bgzipped() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_by_dir_error_no_files_found_not_bgzipped() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_by_list_error_no_files_found() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_multiple_by_dir_bgzipped() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_multiple_by_dir_not_bgzipped() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_multiple_by_list() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_single_already_bgzipped() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_single_by_dir() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_single_by_list() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_merge_vcfs_single_no_copy_needed() (VAPr.tests.test_vcf_merging.TestFunctions method)
test_parse_error_reported_as_warn() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString method)
test_parse_GT_AD_DP_GQ_PL() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString method)
test_parse_GT_GQ_PL() (VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString method)
test_rare_deleterious_variants_all_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_rare_deleterious_variants_specific_samples() (VAPr.tests.test_vapr_core.TestVaprDataset method)
test_read_chunk_of_annotations_to_dicts_list() (VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser method)
test_read_counts_setter() (VAPr.tests.test_vcf_genotype_fields_parsing.TestAllele method)
test_read_counts_setter_error() (VAPr.tests.test_vcf_genotype_fields_parsing.TestAllele method)
TestAllele (class in VAPr.tests.test_vcf_genotype_fields_parsing)
TestAnnotationJobParamsIndices (class in VAPr.tests.test_chunk_processing)
TestAnnovarAnnotatedVariant (class in VAPr.tests.test_annovar_output_parsing)
TestAnnovarTxtParser (class in VAPr.tests.test_annovar_output_parsing)
TestAnnovarWrapper (class in VAPr.tests.test_annovar_running)
TestFunctions (class in VAPr.tests.test_chunk_processing)
(class in VAPr.tests.test_filtering)
(class in VAPr.tests.test_validation)
(class in VAPr.tests.test_vcf_genotype_fields_parsing)
(class in VAPr.tests.test_vcf_merging)
TestGenotypeLikelihood (class in VAPr.tests.test_vcf_genotype_fields_parsing)
TestVaprAnnotator (class in VAPr.tests.test_vapr_core)
TestVaprDataset (class in VAPr.tests.test_vapr_core)
TestVCFGenotypeInfo (class in VAPr.tests.test_vcf_genotype_fields_parsing)
TestVCFGenotypeString (class in VAPr.tests.test_vcf_genotype_fields_parsing)
TFBS_CONS_SITES_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
THOU_G_2015_ALL_HEADER (VAPr.annovar_output_parsing.AnnovarTxtParser attribute)
U
UNFILTERED_ALLELE_DEPTH_TAG (VAPr.vcf_genotype_fields_parsing.VCFGenotypeParser attribute)
unfiltered_read_counts (VAPr.vcf_genotype_fields_parsing.Allele attribute)
unprocessed_info (VAPr.vcf_genotype_fields_parsing.VCFGenotypeInfo attribute)
V
VAPr (module)
VAPr.annovar_output_parsing (module)
VAPr.annovar_running (module)
VAPr.chunk_processing (module)
VAPr.filtering (module)
VAPr.tests (module)
VAPr.tests.test_annovar_output_parsing (module)
VAPr.tests.test_annovar_running (module)
VAPr.tests.test_chunk_processing (module)
VAPr.tests.test_filtering (module)
VAPr.tests.test_validation (module)
VAPr.tests.test_vapr_core (module)
VAPr.tests.test_vcf_genotype_fields_parsing (module)
VAPr.tests.test_vcf_merging (module)
VAPr.validation (module)
VAPr.vapr_core (module)
VAPr.vcf_genotype_fields_parsing (module)
VAPr.vcf_merging (module)
VaprAnnotator (class in VAPr.vapr_core)
VaprDataset (class in VAPr.vapr_core)
VCFGenotypeInfo (class in VAPr.vcf_genotype_fields_parsing)
VCFGenotypeParser (class in VAPr.vcf_genotype_fields_parsing)
VERBOSE_LEVEL_INDEX (VAPr.chunk_processing.AnnotationJobParamsIndices attribute)
W
write_filtered_annotated_csv() (VAPr.vapr_core.VaprDataset method)
write_filtered_annotated_vcf() (VAPr.vapr_core.VaprDataset method)
write_unfiltered_annotated_csv() (VAPr.vapr_core.VaprDataset method)
write_unfiltered_annotated_csvs_per_sample() (VAPr.vapr_core.VaprDataset method)
write_unfiltered_annotated_vcf() (VAPr.vapr_core.VaprDataset method)
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.