Index

_

_abc_impl (src.analyzer.Analyzer attribute) (src.analyzer.BRCAAnalyzer attribute) (src.analyzer.TestAnalyzerhg19 attribute) (src.core.analyzer.adapter_trimmer.AdapterTrimmer attribute) (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator attribute) (src.core.analyzer.annotation_adapter.IAnnotationAdapter attribute) (src.core.analyzer.annotation_adapter.SnpEffAnnotationAdapter attribute) (src.core.analyzer.bam_grouper.BamGrouper attribute) (src.core.analyzer.bqsr_performer.BQSRPerformer attribute) (src.core.analyzer.i_data_preparator.IDataPreparator attribute) (src.core.analyzer.i_variant_caller.IVariantCaller attribute) (src.core.analyzer.primer_cutter.CutPrimers attribute) (src.core.analyzer.primer_cutter.PTrimmer attribute) (src.core.analyzer.sequence_aligner.BWAAligner attribute) (src.core.analyzer.sequence_aligner.SequenceAligner attribute) (src.core.analyzer.variant_caller.FreebayesVariantCaller attribute) (src.core.analyzer.variant_caller.PiscesVariantCaller attribute) (src.core.analyzer.variant_caller.UnifiedGenotyperVariantCaller attribute) (src.core.analyzer.variant_caller.VariantCaller attribute) (src.core.base.CommandExecutor attribute) (src.core.base.ICommandExecutor attribute) (src.core.configurator.argument_parser.ArgumentParser attribute) (src.core.configurator.argument_parser.IArgumentParser attribute) (src.core.configurator.config_loader.ConfigLoader attribute) (src.core.configurator.config_loader.IConfigLoader attribute) (src.core.configurator.logging_configurator.ILoggingConfigurator attribute) (src.core.configurator.logging_configurator.LoggingConfigurator attribute) (src.core.configurator.path_validator.IPathValidator attribute) (src.core.configurator.path_validator.PathValidator attribute) (src.core.sample_data_factory.ISampleDataFactory attribute) (src.core.sample_data_factory.SampleDataFactory attribute) (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter attribute) (src.utils.demultiplexor_adapter.i_demultiplexor_adapter.IDemultiplexorAdapter attribute) (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) (src.utils.report_aggregator.i_report_data_container.IReportDataContainer attribute) (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute) _add_param() (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter method) _check_config() (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter static method)

_instances (src.core.base.SingletonMeta attribute) _is_protocol (src.analyzer.Analyzer attribute) (src.analyzer.BRCAAnalyzer attribute) (src.analyzer.TestAnalyzerhg19 attribute) (src.core.analyzer.adapter_trimmer.AdapterTrimmer attribute) (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator attribute) (src.core.analyzer.annotation_adapter.IAnnotationAdapter attribute) (src.core.analyzer.annotation_adapter.SnpEffAnnotationAdapter attribute) (src.core.analyzer.bam_grouper.BamGrouper attribute) (src.core.analyzer.bqsr_performer.BQSRPerformer attribute) (src.core.analyzer.i_data_preparator.IDataPreparator attribute) (src.core.analyzer.i_variant_caller.IVariantCaller attribute) (src.core.analyzer.primer_cutter.CutPrimers attribute) (src.core.analyzer.primer_cutter.PTrimmer attribute) (src.core.analyzer.sequence_aligner.BWAAligner attribute) (src.core.analyzer.sequence_aligner.SequenceAligner attribute) (src.core.analyzer.variant_caller.FreebayesVariantCaller attribute) (src.core.analyzer.variant_caller.PiscesVariantCaller attribute) (src.core.analyzer.variant_caller.UnifiedGenotyperVariantCaller attribute) (src.core.analyzer.variant_caller.VariantCaller attribute) (src.core.base.CommandExecutor attribute) (src.core.base.ICommandExecutor attribute) (src.core.configurator.argument_parser.ArgumentParser attribute) (src.core.configurator.argument_parser.IArgumentParser attribute) (src.core.configurator.config_loader.ConfigLoader attribute) (src.core.configurator.config_loader.IConfigLoader attribute) (src.core.configurator.logging_configurator.ILoggingConfigurator attribute) (src.core.configurator.logging_configurator.LoggingConfigurator attribute) (src.core.configurator.path_validator.IPathValidator attribute) (src.core.configurator.path_validator.PathValidator attribute) (src.core.sample_data_factory.ISampleDataFactory attribute) (src.core.sample_data_factory.SampleDataFactory attribute) (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter attribute) (src.utils.demultiplexor_adapter.i_demultiplexor_adapter.IDemultiplexorAdapter attribute) _load_configuration() (src.configurator.Configurator method) _parse_args() (src.configurator.Configurator method) (src.configurator.Configurator static method) _setup_logger() (src.configurator.Configurator method) (src.configurator.Configurator static method) _setup_output_directory() (src.configurator.Configurator method), [1]

A

AdapterTrimmer (class in src.core.analyzer.adapter_trimmer) add_section() (src.utils.table_manager.sample_sheet_container.SampleSheetContainer method) Allele (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) allele (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) allele_id (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) alternate (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] aminoacid (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) aminoacid_change (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] AmpliconCoverageDataPreparator (class in src.core.analyzer.amplicon_coverage_computer) analyze() (src.analyzer.Analyzer method), [1] (src.analyzer.BRCAAnalyzer method), [1] (src.analyzer.TestAnalyzerhg19 method)

Analyzer (class in src.analyzer) annotate() (src.core.analyzer.annotation_adapter.IAnnotationAdapter method) (src.core.analyzer.annotation_adapter.SnpEffAnnotationAdapter method) Annotation (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) annotation (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) Annotation_Impact (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) annotation_impact (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) AnnotationDataContainer (class in src.utils.report_aggregator.annotation_data_container) args (src.configurator.Configurator attribute) ArgumentParser (class in src.core.configurator.argument_parser)

B

bam_filepath (src.core.sample_data_container.SampleDataContainer attribute), [1] BamGrouper (class in src.core.analyzer.bam_grouper) BclToFastqAdapter (class in src.utils.demultiplexor_adapter.bcl2fastq_adapter)

BQSRPerformer (class in src.core.analyzer.bqsr_performer) BRCAAnalyzer (class in src.analyzer) build() (src.utils.table_manager.sample_sheet_builder.SampleSheetBuilder method) BWAAligner (class in src.core.analyzer.sequence_aligner)

C

c (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer.HGVS attribute) c_dna (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) call_variant() (src.core.analyzer.i_variant_caller.IVariantCaller method) (src.core.analyzer.variant_caller.FreebayesVariantCaller method), [1] (src.core.analyzer.variant_caller.PiscesVariantCaller method), [1] (src.core.analyzer.variant_caller.UnifiedGenotyperVariantCaller method), [1] (src.core.analyzer.variant_caller.VariantCaller method) caller (src.core.base.CommandExecutor attribute) cds (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) check_reference() (src.dependency_handler.DependencyHandler method) chromosome (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] clinical_sign (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) clinvar (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] ClinvarVariantAnnotationContainer (class in src.utils.report_aggregator.variant_data_container) cmd_caller (src.analyzer.Analyzer attribute) (src.analyzer.BRCAAnalyzer attribute) (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter attribute)

CommandExecutor (class in src.core.base) config (src.configurator.Configurator attribute) (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter attribute) ConfigLoader (class in src.core.configurator.config_loader) ConfigurationError Configurator (class in src.configurator) configurator (src.analyzer.Analyzer attribute) (src.analyzer.BRCAAnalyzer attribute) (src.core.analyzer.variant_caller.VariantCaller attribute) container (src.utils.table_manager.sample_sheet_builder.SampleSheetBuilder attribute) count_indels() (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator static method) count_region_coverage() (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator method) count_target_char() (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator static method) count_variant_coverage() (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator method) create_adapter() (src.utils.demultiplexor_adapter.demultiplexor_adapter_factory.DemultiplexorAdapterFactory static method) create_caller() (src.core.analyzer.variant_caller_factory.VariantCallerFactory static method) create_primer_cutter() (src.core.analyzer.primer_cutter.PrimerCutter static method) CutPrimers (class in src.core.analyzer.primer_cutter)

D

data (src.utils.table_manager.sample_sheet_container.Section attribute), [1] demultiplex() (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter method) (src.utils.demultiplexor_adapter.i_demultiplexor_adapter.IDemultiplexorAdapter method) DemultiplexorAdapterFactory (class in src.utils.demultiplexor_adapter.demultiplexor_adapter_factory) DependencyHandler (class in src.dependency_handler)

depth_filter() (in module src.utils.util) disease_database (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) disease_name (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) Distance (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) distance (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute)

E

end (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] execute() (in module src.core.base) exon (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute)

exonic_function (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] extract_archive() (in module src.core.base) extract_barcodes() (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter method) (src.utils.demultiplexor_adapter.i_demultiplexor_adapter.IDemultiplexorAdapter method)

F

Feature_ID (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) Feature_Type (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute)

fetch_dependency() (src.dependency_handler.DependencyHandler static method) FreebayesVariantCaller (class in src.core.analyzer.variant_caller) from_list() (src.utils.report_aggregator.i_report_data_container.IReportDataContainer class method)

G

gene_detail (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] gene_function (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] Gene_ID (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) gene_id (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) Gene_Name (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) gene_name (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1]

generate_mpileup() (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator method) get_adapter() (src.utils.demultiplexor_adapter.demultiplexor_adapter_factory.DemultiplexorAdapterFactory method) get_lines() (src.utils.table_manager.sample_sheet_builder.SampleSheetBuilder method) get_platform() (in module src.core.base) get_sections() (src.utils.table_manager.sample_sheet_container.SampleSheetContainer method) get_unique_path() (in module src.core.base)

H

hgvs_cds (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute)

hgvs_protein (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute)

I

IAnnotationAdapter (class in src.core.analyzer.annotation_adapter) IArgumentParser (class in src.core.configurator.argument_parser) ICommandExecutor (class in src.core.base) IConfigLoader (class in src.core.configurator.config_loader) IDataPreparator (class in src.core.analyzer.i_data_preparator) IDemultiplexorAdapter (class in src.utils.demultiplexor_adapter.i_demultiplexor_adapter) ILoggingConfigurator (class in src.core.configurator.logging_configurator)

info (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) insert_processing_infix() (in module src.core.base) IPathValidator (class in src.core.configurator.path_validator) IReportDataContainer (class in src.utils.report_aggregator.i_report_data_container) is_module_loaded() (src.dependency_handler.DependencyHandler static method) ISampleDataFactory (class in src.core.sample_data_factory) IVariantCaller (class in src.core.analyzer.i_variant_caller)

L

lines (src.utils.table_manager.sample_sheet_builder.SampleSheetBuilder attribute) load() (src.core.configurator.config_loader.ConfigLoader method) (src.core.configurator.config_loader.IConfigLoader method) log_path (src.configurator.Configurator attribute) logger (src.configurator.Configurator attribute) (src.core.base.CommandExecutor attribute) (src.core.base.LoggerMixin attribute) (src.utils.demultiplexor_adapter.bcl2fastq_adapter.BclToFastqAdapter attribute)

LoggerMixin (class in src.core.base) LoggingConfigurator (class in src.core.configurator.logging_configurator)

M

main() (in module src.demultiplexor_adapter) merge_fastq() (in module src.utils.reads_merger) message (src.core.configurator.configuration_error.ConfigurationError attribute) module src src.analyzer src.configurator src.core src.core.analyzer src.core.analyzer.adapter_trimmer src.core.analyzer.amplicon_coverage_computer src.core.analyzer.annotation_adapter src.core.analyzer.bam_grouper src.core.analyzer.bqsr_performer src.core.analyzer.i_data_preparator src.core.analyzer.i_variant_caller src.core.analyzer.primer_cutter src.core.analyzer.sequence_aligner src.core.analyzer.variant_caller src.core.analyzer.variant_caller_factory src.core.base src.core.configurator src.core.configurator.argument_parser src.core.configurator.config_loader src.core.configurator.configuration_error src.core.configurator.logging_configurator src.core.configurator.path_validator src.core.sample_data_container src.core.sample_data_factory src.demultiplexor_adapter src.dependency_handler src.utils src.utils.demultiplexor_adapter src.utils.demultiplexor_adapter.bcl2fastq_adapter src.utils.demultiplexor_adapter.demultiplexor_adapter_factory src.utils.demultiplexor_adapter.i_demultiplexor_adapter src.utils.reads_merger src.utils.report_aggregator src.utils.report_aggregator.annotation_data_container src.utils.report_aggregator.i_report_data_container src.utils.report_aggregator.variant_data_container src.utils.table_manager src.utils.table_manager.sample_sheet_builder src.utils.table_manager.sample_sheet_container src.utils.util

mutation_id (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) mutation_type (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute)

N

name (src.utils.table_manager.sample_sheet_container.Section attribute), [1]

O

onco_disease_database (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) onco_disease_name (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) onco_review_status (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute)

oncogenicity_factor (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) one_thousand_genomics (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] other_info (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] output_dir (src.configurator.Configurator attribute)

P

p (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer.HGVS attribute) parse() (src.core.configurator.argument_parser.ArgumentParser static method) (src.core.configurator.argument_parser.IArgumentParser static method) parse_args() (in module src.utils.reads_merger) parse_configuration() (src.configurator.Configurator method), [1] parse_regions() (src.core.sample_data_container.SampleDataContainer method) parse_sample_data() (src.core.sample_data_factory.ISampleDataFactory method) (src.core.sample_data_factory.SampleDataFactory method) PathValidator (class in src.core.configurator.path_validator) perform() (src.core.analyzer.adapter_trimmer.AdapterTrimmer method) (src.core.analyzer.amplicon_coverage_computer.AmpliconCoverageDataPreparator method) (src.core.analyzer.bam_grouper.BamGrouper method) (src.core.analyzer.bqsr_performer.BQSRPerformer method) (src.core.analyzer.i_data_preparator.IDataPreparator method) (src.core.analyzer.primer_cutter.CutPrimers method) (src.core.analyzer.primer_cutter.PTrimmer method) (src.core.analyzer.sequence_aligner.BWAAligner method) (src.core.analyzer.sequence_aligner.SequenceAligner method)

PiscesVariantCaller (class in src.core.analyzer.variant_caller) PositionNotFoundError prepare_data() (src.analyzer.Analyzer method), [1] (src.analyzer.BRCAAnalyzer method), [1] (src.analyzer.TestAnalyzerhg19 method) PrimerCutter (class in src.core.analyzer.primer_cutter) processing_logpath (src.core.sample_data_container.SampleDataContainer attribute), [1] processing_path (src.core.sample_data_container.SampleDataContainer attribute), [1] PTrimmer (class in src.core.analyzer.primer_cutter)

R

r1_source (src.core.sample_data_container.SampleDataContainer attribute), [1] r2_source (src.core.sample_data_container.SampleDataContainer attribute), [1] Rank (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) reference (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1] reg_tuple_generator() (in module src.utils.util)

report_path (src.core.sample_data_container.SampleDataContainer attribute), [1] resolve_file_path_by_extensions() (src.dependency_handler.DependencyHandler static method) review_status (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) run() (src.core.base.CommandExecutor method) (src.core.base.ICommandExecutor method)

S

SampleDataContainer (class in src.core.sample_data_container) SampleDataFactory (class in src.core.sample_data_factory) SampleSheetBuilder (class in src.utils.table_manager.sample_sheet_builder) SampleSheetContainer (class in src.utils.table_manager.sample_sheet_container) save_to_csv() (src.utils.table_manager.sample_sheet_builder.SampleSheetBuilder method) Section (class in src.utils.table_manager.sample_sheet_container) sections (src.utils.table_manager.sample_sheet_container.SampleSheetContainer attribute), [1] separator (src.utils.table_manager.sample_sheet_builder.SampleSheetBuilder attribute) SequenceAligner (class in src.core.analyzer.sequence_aligner) set_logger() (src.core.base.LoggerMixin method) (src.core.configurator.logging_configurator.ILoggingConfigurator method) (src.core.configurator.logging_configurator.LoggingConfigurator method) (src.dependency_handler.DependencyHandler method) sid (src.core.sample_data_container.SampleDataContainer attribute), [1] SingletonMeta (class in src.core.base) SnpEffAnnotationAdapter (class in src.core.analyzer.annotation_adapter) somatic_clinical_impact (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) somatic_clinical_impact_disease_database (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) somatic_clinical_impact_disease_name (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) somatic_clinical_impact_review_status (src.utils.report_aggregator.variant_data_container.ClinvarVariantAnnotationContainer attribute) src module src.analyzer module src.configurator module src.core module src.core.analyzer module src.core.analyzer.adapter_trimmer module src.core.analyzer.amplicon_coverage_computer module src.core.analyzer.annotation_adapter module src.core.analyzer.bam_grouper module src.core.analyzer.bqsr_performer module src.core.analyzer.i_data_preparator module src.core.analyzer.i_variant_caller module src.core.analyzer.primer_cutter module src.core.analyzer.sequence_aligner module src.core.analyzer.variant_caller module src.core.analyzer.variant_caller_factory module

src.core.base module src.core.configurator module src.core.configurator.argument_parser module src.core.configurator.config_loader module src.core.configurator.configuration_error module src.core.configurator.logging_configurator module src.core.configurator.path_validator module src.core.sample_data_container module src.core.sample_data_factory module src.demultiplexor_adapter module src.dependency_handler module src.utils module src.utils.demultiplexor_adapter module src.utils.demultiplexor_adapter.bcl2fastq_adapter module src.utils.demultiplexor_adapter.demultiplexor_adapter_factory module src.utils.demultiplexor_adapter.i_demultiplexor_adapter module src.utils.reads_merger module src.utils.report_aggregator module src.utils.report_aggregator.annotation_data_container module src.utils.report_aggregator.i_report_data_container module src.utils.report_aggregator.variant_data_container module src.utils.table_manager module src.utils.table_manager.sample_sheet_builder module src.utils.table_manager.sample_sheet_container module src.utils.util module start (src.utils.report_aggregator.variant_data_container.VariantDataContainer attribute), [1]

T

target_regions (src.core.sample_data_container.SampleDataContainer attribute) TestAnalyzerhg19 (class in src.analyzer) to_dict() (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer method) (src.utils.report_aggregator.i_report_data_container.IReportDataContainer class method)

touch() (in module src.core.base) Transcript_BioType (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) transcript_biotype (src.utils.report_aggregator.annotation_data_container.AnnotationDataContainer attribute) try_to_install_module() (src.dependency_handler.DependencyHandler static method)

U

UnifiedGenotyperVariantCaller (class in src.core.analyzer.variant_caller)

V

VariantCaller (class in src.core.analyzer.variant_caller) VariantCallerFactory (class in src.core.analyzer.variant_caller_factory) VariantDataContainer (class in src.utils.report_aggregator.variant_data_container)

vcf_filepath (src.core.sample_data_container.SampleDataContainer attribute), [1] verify_path() (src.core.configurator.path_validator.IPathValidator method) (src.core.configurator.path_validator.PathValidator method) (src.dependency_handler.DependencyHandler static method)