Index

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__enter__() (variantcentrifuge.checkpoint.AtomicFileOperation method) (variantcentrifuge.checkpoint.CheckpointContext method) __exit__() (variantcentrifuge.checkpoint.AtomicFileOperation method) (variantcentrifuge.checkpoint.CheckpointContext method) __getstate__() (variantcentrifuge.checkpoint.PipelineState method)

__init__() (variantcentrifuge.checkpoint.AtomicFileOperation method) (variantcentrifuge.checkpoint.CheckpointContext method) (variantcentrifuge.checkpoint.FileInfo method) (variantcentrifuge.checkpoint.PipelineState method) (variantcentrifuge.checkpoint.StepInfo method) __setstate__() (variantcentrifuge.checkpoint.PipelineState method)

A

add_input_file() (variantcentrifuge.checkpoint.CheckpointContext method) add_links_to_table() (in module variantcentrifuge.links) add_output_file() (variantcentrifuge.checkpoint.CheckpointContext method) aggregate_phenotypes_for_samples() (in module variantcentrifuge.phenotype) analyze_variants() (in module variantcentrifuge.analyze_variants)

annotate_variants_with_gene_lists() (in module variantcentrifuge.helpers) append_tsv_as_sheet() (in module variantcentrifuge.converter) apply_bcftools_prefilter() (in module variantcentrifuge.filters) apply_snpsift_filter() (in module variantcentrifuge.filters) assign_case_control_counts() (in module variantcentrifuge.helpers) AtomicFileOperation (class in variantcentrifuge.checkpoint)

B

build_sample_phenotype_map() (in module variantcentrifuge.helpers)

C

can_resume() (variantcentrifuge.checkpoint.PipelineState method) can_resume_from_stage() (variantcentrifuge.checkpoint.PipelineState method) check_external_tools() (in module variantcentrifuge.utils) check_file() (in module variantcentrifuge.helpers) checkpoint() (in module variantcentrifuge.checkpoint) CheckpointContext (class in variantcentrifuge.checkpoint) checksum (variantcentrifuge.checkpoint.FileInfo attribute) cleanup_stale_stages() (variantcentrifuge.checkpoint.PipelineState method) clear_step_completion() (variantcentrifuge.checkpoint.PipelineState method)

command_hash (variantcentrifuge.checkpoint.StepInfo attribute) complete_step() (variantcentrifuge.checkpoint.PipelineState method) compute_base_name() (in module variantcentrifuge.utils) compute_basic_stats() (in module variantcentrifuge.stats) compute_custom_stats() (in module variantcentrifuge.stats) compute_gene_stats() (in module variantcentrifuge.stats) compute_impact_summary() (in module variantcentrifuge.stats) compute_phenotype_based_case_control_assignment() (in module variantcentrifuge.helpers) compute_variant_type_summary() (in module variantcentrifuge.stats) convert_to_excel() (in module variantcentrifuge.converter)

D

determine_case_control_sets() (in module variantcentrifuge.helpers)

dump_df_to_xlsx() (in module variantcentrifuge.helpers) duration (variantcentrifuge.checkpoint.StepInfo property)

E

end_time (variantcentrifuge.checkpoint.StepInfo attribute) ensure_fields_in_extract() (in module variantcentrifuge.utils) error (variantcentrifuge.checkpoint.StepInfo attribute) extract_fields() (in module variantcentrifuge.extractor)

extract_gencode_id() (in module variantcentrifuge.helpers) extract_phenotypes_for_gt_row() (in module variantcentrifuge.phenotype) extract_sample_and_genotype() (in module variantcentrifuge.helpers) extract_variants() (in module variantcentrifuge.filters)

F

fail_step() (variantcentrifuge.checkpoint.PipelineState method) FileInfo (class in variantcentrifuge.checkpoint) filter_dataframe_with_query() (in module variantcentrifuge.filters) filter_final_tsv_by_genotype() (in module variantcentrifuge.filters) filter_tsv_with_expression() (in module variantcentrifuge.filters)

finalize_excel_file() (in module variantcentrifuge.converter) finalize_step() (variantcentrifuge.checkpoint.PipelineState method) format_phenotypes_like_gt_column() (in module variantcentrifuge.phenotype) from_dict() (variantcentrifuge.checkpoint.StepInfo class method) from_file() (variantcentrifuge.checkpoint.FileInfo class method)

G

generate_html_report() (in module variantcentrifuge.generate_html_report) generate_igv_report() (in module variantcentrifuge.generate_igv_report) generate_igv_safe_filename_base() (in module variantcentrifuge.utils) genotype_to_allele_count() (in module variantcentrifuge.helpers) get_available_resume_points() (variantcentrifuge.checkpoint.PipelineState method) get_completed_stages() (variantcentrifuge.checkpoint.PipelineState method) get_detailed_status() (variantcentrifuge.checkpoint.PipelineState method) get_gene_bed() (in module variantcentrifuge.gene_bed)

get_resume_point() (variantcentrifuge.checkpoint.PipelineState method) get_stages_to_execute() (variantcentrifuge.checkpoint.PipelineState method) get_summary() (variantcentrifuge.checkpoint.PipelineState method) get_tool_version() (in module variantcentrifuge.utils) get_vcf_names() (in module variantcentrifuge.helpers) get_vcf_regions() (in module variantcentrifuge.helpers) get_vcf_samples() (in module variantcentrifuge.helpers) get_vcf_size() (in module variantcentrifuge.helpers)

I

initialize() (variantcentrifuge.checkpoint.PipelineState method)

input_files (variantcentrifuge.checkpoint.StepInfo attribute)

L

load() (variantcentrifuge.checkpoint.PipelineState method) load_config() (in module variantcentrifuge.config)

load_gene_list() (in module variantcentrifuge.helpers) load_phenotypes() (in module variantcentrifuge.phenotype)

M

match_IGV_link_columns() (in module variantcentrifuge.helpers) merge_and_format_stats() (in module variantcentrifuge.stats) module variantcentrifuge.analyze_variants variantcentrifuge.checkpoint variantcentrifuge.config variantcentrifuge.converter variantcentrifuge.extractor variantcentrifuge.filters variantcentrifuge.gene_bed variantcentrifuge.gene_burden variantcentrifuge.generate_html_report variantcentrifuge.generate_igv_report variantcentrifuge.helpers variantcentrifuge.links variantcentrifuge.phenotype variantcentrifuge.replacer variantcentrifuge.stats variantcentrifuge.utils variantcentrifuge.validators

mtime (variantcentrifuge.checkpoint.FileInfo attribute)

N

name (variantcentrifuge.checkpoint.StepInfo attribute)

normalize_genes() (in module variantcentrifuge.gene_bed) normalize_vcf_headers() (in module variantcentrifuge.utils)

O

output_files (variantcentrifuge.checkpoint.StepInfo attribute)

P

parameters (variantcentrifuge.checkpoint.StepInfo attribute) parse_bam_mapping() (in module variantcentrifuge.generate_igv_report) path (variantcentrifuge.checkpoint.FileInfo attribute)

perform_gene_burden_analysis() (in module variantcentrifuge.gene_burden) PipelineState (class in variantcentrifuge.checkpoint) produce_report_json() (in module variantcentrifuge.converter)

R

read_sequencing_manifest() (in module variantcentrifuge.helpers) remove_vcf_extensions() (in module variantcentrifuge.utils)

replace_genotypes() (in module variantcentrifuge.replacer) run_command() (in module variantcentrifuge.utils)

S

sanitize_metadata_field() (in module variantcentrifuge.utils) save() (variantcentrifuge.checkpoint.PipelineState method) should_skip_step() (variantcentrifuge.checkpoint.PipelineState method) size (variantcentrifuge.checkpoint.FileInfo attribute) smart_open() (in module variantcentrifuge.utils) split_bed_file() (in module variantcentrifuge.utils)

start_step() (variantcentrifuge.checkpoint.PipelineState method) start_time (variantcentrifuge.checkpoint.StepInfo attribute) STATE_FILE_NAME (variantcentrifuge.checkpoint.PipelineState attribute) STATE_VERSION (variantcentrifuge.checkpoint.PipelineState attribute) status (variantcentrifuge.checkpoint.StepInfo attribute) StepInfo (class in variantcentrifuge.checkpoint)

T

to_dict() (variantcentrifuge.checkpoint.StepInfo method)

V

validate() (variantcentrifuge.checkpoint.FileInfo method) validate_igv_files() (in module variantcentrifuge.validators) validate_mandatory_parameters() (in module variantcentrifuge.validators) validate_phenotype_file() (in module variantcentrifuge.validators) validate_resume_from_stage() (variantcentrifuge.checkpoint.PipelineState method) validate_vcf_file() (in module variantcentrifuge.validators) variantcentrifuge.analyze_variants module variantcentrifuge.checkpoint module variantcentrifuge.config module variantcentrifuge.converter module variantcentrifuge.extractor module variantcentrifuge.filters module variantcentrifuge.gene_bed module

variantcentrifuge.gene_burden module variantcentrifuge.generate_html_report module variantcentrifuge.generate_igv_report module variantcentrifuge.helpers module variantcentrifuge.links module variantcentrifuge.phenotype module variantcentrifuge.replacer module variantcentrifuge.stats module variantcentrifuge.utils module variantcentrifuge.validators module