Index
_
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A
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B
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C
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D
|
E
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F
|
G
|
I
|
K
|
L
|
M
|
O
|
P
|
R
|
S
|
T
|
U
|
V
_
__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)
Bowtie2AlignStep (class in camparee.bowtie2)
Bowtie2IndexStep (class in camparee.bowtie2)
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.bowtie2 (module)
camparee.camparee_constants (module)
camparee.camparee_controller (module)
camparee.camparee_step_provider (module)
camparee.camparee_utils (module)
camparee.expression_pipeline (module)
camparee.genome_alignment (module)
camparee.genome_builder (module)
camparee.intron_quant (module)
camparee.kallisto (module)
camparee.molecule_maker (module)
camparee.transcript_gene_quant (module)
camparee.transcriptome_fasta_preparation (module)
camparee.update_annotation_for_genome (module)
camparee.variants_compilation (module)
camparee.variants_finder (module)
CampareeConstants (in module camparee.camparee_constants)
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_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.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep method)
create_exon_sequence_map() (camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep method)
create_genome() (camparee.camparee_utils.CampareeUtils static method)
create_oneline_seq_fasta() (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)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep method)
D
delete_segment() (camparee.genome_builder.Genome method)
description (camparee.genome_builder.SingleInstanceVariant attribute)
(camparee.variants_finder.Read attribute)
E
execute() (camparee.abstract_camparee_step.AbstractCampareeStep method)
(camparee.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method)
(camparee.beagle.BeagleStep method)
(camparee.bowtie2.Bowtie2AlignStep method)
(camparee.bowtie2.Bowtie2IndexStep method)
(camparee.genome_alignment.GenomeAlignmentStep method)
(camparee.genome_alignment.GenomeBamIndexStep method)
(camparee.genome_builder.GenomeBuilderStep method)
(camparee.intron_quant.IntronQuantificationStep method)
(camparee.kallisto.KallistoIndexStep method)
(camparee.kallisto.KallistoQuantStep method)
(camparee.molecule_maker.MoleculeMakerStep method)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep method)
(camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep 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)
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.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method)
(camparee.beagle.BeagleStep method)
(camparee.bowtie2.Bowtie2AlignStep method)
(camparee.bowtie2.Bowtie2IndexStep method)
(camparee.genome_alignment.GenomeAlignmentStep method)
(camparee.genome_alignment.GenomeBamIndexStep method)
(camparee.genome_builder.GenomeBuilderStep method)
(camparee.intron_quant.IntronQuantificationStep method)
(camparee.kallisto.KallistoIndexStep method)
(camparee.kallisto.KallistoQuantStep method)
(camparee.molecule_maker.MoleculeMakerStep method)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep method)
(camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep 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_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.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method)
(camparee.beagle.BeagleStep method)
(camparee.bowtie2.Bowtie2AlignStep method)
(camparee.bowtie2.Bowtie2IndexStep method)
(camparee.genome_alignment.GenomeAlignmentStep method)
(camparee.genome_alignment.GenomeBamIndexStep method)
(camparee.genome_builder.GenomeBuilderStep method)
(camparee.intron_quant.IntronQuantificationStep method)
(camparee.kallisto.KallistoIndexStep method)
(camparee.kallisto.KallistoQuantStep method)
(camparee.molecule_maker.MoleculeMakerStep method)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep method)
(camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep 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.allelic_imbalance_quant.AllelicImbalanceQuantificationStep static method)
(camparee.beagle.BeagleStep static method)
(camparee.bowtie2.Bowtie2AlignStep static method)
(camparee.bowtie2.Bowtie2IndexStep 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.kallisto.KallistoIndexStep static method)
(camparee.kallisto.KallistoQuantStep static method)
(camparee.molecule_maker.MoleculeMakerStep static method)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep static method)
(camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep static method)
(camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep static method)
(camparee.variants_compilation.VariantsCompilationStep static method)
(camparee.variants_finder.VariantsFinderStep static method)
K
KallistoIndexStep (class in camparee.kallisto)
KallistoQuantStep (class in camparee.kallisto)
L
list_supported_camparee_steps() (camparee.camparee_step_provider.CampareeStepProvider method)
load_allelic_quants() (camparee.molecule_maker.MoleculeMakerStep method)
load_gene_quants() (camparee.molecule_maker.MoleculeMakerStep method)
load_indels() (camparee.molecule_maker.MoleculeMakerStep method)
load_intron_quants() (camparee.molecule_maker.MoleculeMakerStep method)
load_isoform_quants() (camparee.molecule_maker.MoleculeMakerStep 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.bowtie2.Bowtie2AlignStep static method)
(camparee.bowtie2.Bowtie2IndexStep 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.kallisto.KallistoIndexStep static method)
(camparee.kallisto.KallistoQuantStep static method)
(camparee.molecule_maker.MoleculeMakerStep static method)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep static method)
(camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep 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.MoleculeMakerStep 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)
MoleculeMakerStep (class in camparee.molecule_maker)
O
open_file() (camparee.camparee_utils.CampareeUtils static method)
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)
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.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep 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)
TranscriptGeneQuantificationStep (class in camparee.transcript_gene_quant)
TranscriptomeFastaPreparationStep (class in camparee.transcriptome_fasta_preparation)
TranscriptRegion (class in camparee.annotation_info)
trim_annotation_file() (camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep method)
U
UpdateAnnotationForGenomeStep (class in camparee.update_annotation_for_genome)
V
validate() (camparee.abstract_camparee_step.AbstractCampareeStep method)
(camparee.allelic_imbalance_quant.AllelicImbalanceQuantificationStep method)
(camparee.beagle.BeagleStep method)
(camparee.bowtie2.Bowtie2AlignStep method)
(camparee.bowtie2.Bowtie2IndexStep method)
(camparee.genome_alignment.GenomeAlignmentStep method)
(camparee.genome_alignment.GenomeBamIndexStep method)
(camparee.genome_builder.GenomeBuilderStep method)
(camparee.intron_quant.IntronQuantificationStep method)
(camparee.kallisto.KallistoIndexStep method)
(camparee.kallisto.KallistoQuantStep method)
(camparee.molecule_maker.MoleculeMakerStep method)
(camparee.transcript_gene_quant.TranscriptGeneQuantificationStep method)
(camparee.transcriptome_fasta_preparation.TranscriptomeFastaPreparationStep method)
(camparee.update_annotation_for_genome.UpdateAnnotationForGenomeStep method)
(camparee.variants_compilation.VariantsCompilationStep method)
(camparee.variants_finder.VariantsFinderStep method)
validate_and_set_optional_inputs() (camparee.expression_pipeline.ExpressionPipeline method)
validate_and_set_output_data() (camparee.expression_pipeline.ExpressionPipeline method)
validate_and_set_resources() (camparee.expression_pipeline.ExpressionPipeline method)
validate_and_set_sample_optional_inputs() (camparee.expression_pipeline.ExpressionPipeline method)
validate_samples() (camparee.camparee_controller.CampareeController method)
VariantsCompilationStep (class in camparee.variants_compilation)
VariantsFinderStep (class in camparee.variants_finder)
CAMPAREE
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