Index

_

__steps (camparee.camparee_step_provider.CampareeStepProvider attribute)

A

AbstractCampareeStep (class in camparee.abstract_camparee_step) add_flanks() (camparee.annotation_info.AnnotationInfo method) AllelicImbalanceQuantificationStep (class in camparee.allelic_imbalance_quant)

AnnotationInfo (class in camparee.annotation_info) append_segment() (camparee.genome_builder.Genome method) assemble_input_samples() (camparee.camparee_controller.CampareeController method)

B

BeagleStep (class in camparee.beagle)

build_sequence_from_variant() (camparee.genome_builder.GenomeBuilderStep method)

C

calculate_entropy() (camparee.variants_finder.PositionInfo method) call_variants() (camparee.variants_finder.VariantsFinderStep method) camparee.abstract_camparee_step (module) camparee.allelic_imbalance_quant (module) camparee.annotation_info (module) camparee.beagle (module) camparee.camparee_controller (module) camparee.camparee_step_provider (module) camparee.camparee_utils (module) camparee.expression_pipeline (module) camparee.gene_files_preparation (module) camparee.genome_alignment (module) camparee.genome_builder (module) camparee.intron_quant (module) camparee.molecule_maker (module) camparee.run_pysam_index (module) camparee.transcriptomes (module) camparee.update_annotation_for_genome (module) camparee.variants_compilation (module)

camparee.variants_finder (module) CampareeController (class in camparee.camparee_controller) CampareeException CampareeStepProvider (class in camparee.camparee_step_provider) CampareeStepProviderException CampareeUtils (class in camparee.camparee_utils) CampareeUtilsException CampareeValidationException check_file_existence() (camparee.camparee_controller.CampareeController static method) chromosome (camparee.genome_builder.SingleInstanceVariant attribute) collect_reads() (camparee.variants_finder.VariantsFinderStep method) convert_genome_position_to_reference() (camparee.molecule_maker.MoleculeMaker method) convert_gtf_to_annot_file_format() (camparee.camparee_utils.CampareeUtils static method) create_chr_ploidy_data() (camparee.camparee_utils.CampareeUtils static method) create_controller_log() (camparee.camparee_controller.CampareeController method) create_exon_location_list() (camparee.gene_files_preparation.GeneFilesPreparation method) create_exon_sequence_map() (camparee.gene_files_preparation.GeneFilesPreparation method) create_genome() (camparee.camparee_utils.CampareeUtils static method) create_output_folder_structure() (camparee.camparee_controller.CampareeController method) create_transcript_gene_map() (camparee.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method)

D

delete_segment() (camparee.genome_builder.Genome method)

description (camparee.genome_builder.SingleInstanceVariant attribute) (camparee.variants_finder.Read attribute)

E

edit_reference_genome() (camparee.camparee_utils.CampareeUtils static method) execute() (camparee.abstract_camparee_step.AbstractCampareeStep method) (camparee.beagle.BeagleStep method) (camparee.genome_alignment.GenomeAlignmentStep method) (camparee.genome_alignment.GenomeBamIndexStep method) (camparee.genome_builder.GenomeBuilderStep method) (camparee.intron_quant.IntronQuantificationStep method) (camparee.transcriptomes.TranscriptQuantificatAndMoleculeGenerationStep method) (camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep method) (camparee.variants_compilation.VariantsCompilationStep method) (camparee.variants_finder.VariantsFinderStep method)

ExpressionPipeline (class in camparee.expression_pipeline)

F

filter_chromosome_list() (camparee.variants_finder.VariantsFinderStep method)

filter_reads() (camparee.variants_finder.PositionInfo method)

G

Gene (class in camparee.annotation_info) GeneFilesPreparation (class in camparee.gene_files_preparation) generate_job_seeds() (camparee.expression_pipeline.ExpressionPipeline method) Genome (class in camparee.genome_builder) GenomeAlignmentStep (class in camparee.genome_alignment) GenomeBamIndexStep (class in camparee.genome_alignment) GenomeBuilderStep (class in camparee.genome_builder) get() (camparee.camparee_step_provider.CampareeStepProvider method) get_commandline_call() (camparee.abstract_camparee_step.AbstractCampareeStep method) (camparee.beagle.BeagleStep method) (camparee.genome_alignment.GenomeAlignmentStep method) (camparee.genome_alignment.GenomeBamIndexStep method) (camparee.genome_builder.GenomeBuilderStep method) (camparee.intron_quant.IntronQuantificationStep method) (camparee.transcriptomes.TranscriptQuantificatAndMoleculeGenerationStep method) (camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep method) (camparee.variants_compilation.VariantsCompilationStep method) (camparee.variants_finder.VariantsFinderStep method)

get_genome_bam_path() (camparee.genome_alignment.GenomeAlignmentStep method) get_missing_chr_list() (camparee.genome_builder.GenomeBuilderStep method) get_paired_chr_list() (camparee.genome_builder.GenomeBuilderStep method) get_reference_cigar() (camparee.molecule_maker.MoleculeMaker method) get_unpaired_chr_list() (camparee.genome_builder.GenomeBuilderStep method) get_unpaired_chr_variant_data() (camparee.genome_builder.GenomeBuilderStep method) get_validation_attributes() (camparee.abstract_camparee_step.AbstractCampareeStep method) (camparee.beagle.BeagleStep method) (camparee.genome_alignment.GenomeAlignmentStep method) (camparee.genome_alignment.GenomeBamIndexStep method) (camparee.genome_builder.GenomeBuilderStep method) (camparee.intron_quant.IntronQuantificationStep method) (camparee.transcriptomes.TranscriptQuantificatAndMoleculeGenerationStep method) (camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep method) (camparee.variants_compilation.VariantsCompilationStep method) (camparee.variants_finder.VariantsFinderStep method) group_data() (camparee.genome_builder.GenomeBuilderStep static method)

I

identify_variant() (camparee.variants_finder.VariantsFinderStep method) insert_segment() (camparee.genome_builder.Genome method) Intron (class in camparee.annotation_info) IntronQuantificationStep (class in camparee.intron_quant) is_output_valid() (camparee.abstract_camparee_step.AbstractCampareeStep static method) (camparee.beagle.BeagleStep static method) (camparee.genome_alignment.GenomeAlignmentStep static method) (camparee.genome_alignment.GenomeBamIndexStep static method) (camparee.genome_builder.GenomeBuilderStep static method) (camparee.intron_quant.IntronQuantificationStep static method) (camparee.transcriptomes.TranscriptQuantificatAndMoleculeGenerationStep static method) (camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep static method) (camparee.variants_compilation.VariantsCompilationStep static method) (camparee.variants_finder.VariantsFinderStep static method)

L

list_supported_camparee_steps() (camparee.camparee_step_provider.CampareeStepProvider method) load_allelic_quants() (camparee.molecule_maker.MoleculeMaker method) load_gene_quants() (camparee.molecule_maker.MoleculeMaker method) load_genome() (camparee.molecule_maker.MoleculeMaker method) load_indels() (camparee.molecule_maker.MoleculeMaker method)

load_intron_quants() (camparee.molecule_maker.MoleculeMaker method) load_isoform_quants() (camparee.molecule_maker.MoleculeMaker method) load_transcriptome() (camparee.molecule_maker.MoleculeMaker method) load_variants() (camparee.variants_finder.VariantsFinderStep method) locate_sample() (camparee.genome_builder.GenomeBuilderStep method)

M

main() (camparee.abstract_camparee_step.AbstractCampareeStep static method) (camparee.allelic_imbalance_quant.AllelicImbalanceQuantificationStep static method) (camparee.beagle.BeagleStep static method) (camparee.gene_files_preparation.GeneFilesPreparation static method) (camparee.genome_alignment.GenomeAlignmentStep static method) (camparee.genome_alignment.GenomeBamIndexStep static method) (camparee.genome_builder.GenomeBuilderStep static method) (camparee.intron_quant.IntronQuantificationStep static method) (camparee.transcriptomes.TranscriptQuantificatAndMoleculeGenerationStep static method) (camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep static method) (camparee.variants_compilation.VariantsCompilationStep static method) (camparee.variants_finder.VariantsFinderStep static method)

make_molecule_file() (camparee.molecule_maker.MoleculeMaker method) make_paired_chromosome() (camparee.genome_builder.GenomeBuilderStep method) make_reference_chromosome() (camparee.genome_builder.GenomeBuilderStep method) make_unpaired_chromosome() (camparee.genome_builder.GenomeBuilderStep method) Mintron (class in camparee.annotation_info) MoleculeMaker (class in camparee.molecule_maker)

P

parse_variant_line() (camparee.camparee_utils.CampareeUtils static method) perform_setup() (camparee.camparee_controller.CampareeController method) plant_seed() (camparee.camparee_controller.CampareeController method)

position (camparee.genome_builder.SingleInstanceVariant attribute) (camparee.variants_finder.Read attribute) PositionInfo (class in camparee.variants_finder) prepare_gene_files() (camparee.gene_files_preparation.GeneFilesPreparation method)

Q

quantify_allelic_imbalance() (camparee.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method)

R

Read (class in camparee.variants_finder) read_info() (camparee.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method) Region (class in camparee.annotation_info) register_step() (camparee.camparee_step_provider.CampareeStepProvider method)

remove_clips() (camparee.variants_finder.VariantsFinderStep method) retrieve_configuration() (camparee.camparee_controller.CampareeController method) run_camparee_pipeline() (camparee.camparee_controller.CampareeController method) run_step() (camparee.expression_pipeline.ExpressionPipeline method)

S

save_to_file() (camparee.genome_builder.Genome method) scrub_genome_fasta_file() (camparee.gene_files_preparation.GeneFilesPreparation method)

set_run_id() (camparee.camparee_controller.CampareeController method) set_third_party_software() (camparee.expression_pipeline.ExpressionPipeline method) SingleInstanceVariant (class in camparee.genome_builder)

T

Transcript (class in camparee.annotation_info)

TranscriptQuantificatAndMoleculeGenerationStep (class in camparee.transcriptomes) TranscriptRegion (class in camparee.annotation_info)

U

update_geneinfo_file() (camparee.gene_files_preparation.GeneFilesPreparation method)

UpdateAnnotationForGenomeStep (class in camparee.update_annotation_for_genome)

V

validate() (camparee.abstract_camparee_step.AbstractCampareeStep method) (camparee.beagle.BeagleStep method) (camparee.genome_alignment.GenomeAlignmentStep method) (camparee.genome_alignment.GenomeBamIndexStep method) (camparee.genome_builder.GenomeBuilderStep method) (camparee.intron_quant.IntronQuantificationStep method) (camparee.transcriptomes.TranscriptQuantificatAndMoleculeGenerationStep method) (camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep method) (camparee.variants_compilation.VariantsCompilationStep method) (camparee.variants_finder.VariantsFinderStep method)

validate_and_set_output_data() (camparee.expression_pipeline.ExpressionPipeline method) validate_and_set_resources() (camparee.expression_pipeline.ExpressionPipeline method) validate_samples() (camparee.camparee_controller.CampareeController method) VariantsCompilationStep (class in camparee.variants_compilation) VariantsFinderStep (class in camparee.variants_finder)