Index

A

AdapterLigationStep (class in beers.library_prep.adapter_ligation_step) apply_three_prime_bias() (beers.library_prep.polya_step.PolyAStep method)

assign_coordinates() (beers.cluster.Cluster method) assign_id() (beers.library_prep.pcr_amplification_step.PCRAmplificationStep method)

B

base_counts (beers.cluster.Cluster attribute) beers.cluster module beers.cluster_packet module beers.fast_q module beers.flowcell module beers.library_prep.adapter_ligation_step module beers.library_prep.first_strand_synthesis_step module beers.library_prep.fragment_step module beers.library_prep.library_prep_pipeline module beers.library_prep.pcr_amplification_step module

beers.library_prep.polya_step module beers.library_prep.second_strand_synthesis_step module beers.library_prep.sizing_step module beers.sam module beers.sequence.bridge_amplification_step module beers.sequence.sequence_by_synthesis_step module beers.sequence.sequence_pipeline module BeersLibraryPrepValidationException BeersSequenceValidationException BridgeAmplificationStep (class in beers.sequence.bridge_amplification_step)

C

call_bases() (beers.sequence.sequence_by_synthesis_step.SequenceBySynthesisStep method) called_barcode (beers.cluster.Cluster attribute) called_sequences (beers.cluster.Cluster attribute) Cluster (class in beers.cluster)

cluster_id (beers.cluster.Cluster attribute) ClusterPacket (class in beers.cluster_packet) consumed_coordinates (beers.flowcell.FlowcellLane attribute) convert_molecule_pkt_to_cluster_pkt() (beers.flowcell.Flowcell method) coordinates (beers.cluster.Cluster attribute)

D

deserialize() (beers.cluster.Cluster static method) (beers.cluster_packet.ClusterPacket static method)

diameter (beers.cluster.Cluster attribute)

E

encode_sequence_identifier() (beers.cluster.Cluster method) execute() (beers.library_prep.library_prep_pipeline.LibraryPrepPipeline method) (beers.library_prep.pcr_amplification_step.PCRAmplificationStep method) (beers.sequence.bridge_amplification_step.BridgeAmplificationStep method) (beers.sequence.sequence_by_synthesis_step.SequenceBySynthesisStep method) (beers.sequence.sequence_pipeline.SequencePipeline method)

F

FastQ (class in beers.fast_q) FirstStrandSynthesisStep (class in beers.library_prep.first_strand_synthesis_step)

Flowcell (class in beers.flowcell) FlowcellLane (class in beers.flowcell) FragmentStep (class in beers.library_prep.fragment_step)

G

generate_coordinates_distinct() (beers.flowcell.Flowcell method) generate_coordinates_random() (beers.flowcell.Flowcell method) generate_fasta_header() (beers.cluster.Cluster method) generate_report() (beers.fast_q.FastQ method) (beers.sam.SAM method)

get_base_counts_by_position() (beers.cluster.Cluster method) get_frac_skipped_py() (in module beers.sequence.sequence_by_synthesis_step) get_inv_phasing_matrix() (in module beers.sequence.sequence_by_synthesis_step)

H

hypergeometric() (in module beers.library_prep.pcr_amplification_step)

I

initialize_base_counts() (beers.cluster.Cluster method)

L

lane (beers.cluster.Cluster attribute) (beers.flowcell.FlowcellLane attribute)

LibraryPrepPipeline (class in beers.library_prep.library_prep_pipeline) load_flowcell() (beers.flowcell.Flowcell method)

M

main() (beers.library_prep.library_prep_pipeline.LibraryPrepPipeline static method) (beers.sequence.sequence_pipeline.SequencePipeline static method) module beers.cluster beers.cluster_packet beers.fast_q beers.flowcell beers.library_prep.adapter_ligation_step beers.library_prep.first_strand_synthesis_step beers.library_prep.fragment_step beers.library_prep.library_prep_pipeline beers.library_prep.pcr_amplification_step beers.library_prep.polya_step beers.library_prep.second_strand_synthesis_step beers.library_prep.sizing_step beers.sam beers.sequence.bridge_amplification_step beers.sequence.sequence_by_synthesis_step beers.sequence.sequence_pipeline

molecule (beers.cluster.Cluster attribute) molecule_count (beers.cluster.Cluster attribute) multinomial() (in module beers.sequence.bridge_amplification_step)

P

PCRAmplificationStep (class in beers.library_prep.pcr_amplification_step)

PolyAStep (class in beers.library_prep.polya_step) print_summary() (beers.library_prep.library_prep_pipeline.LibraryPrepPipeline method)

Q

quality_scores (beers.cluster.Cluster attribute)

R

read_cigars (beers.cluster.Cluster attribute) read_flourescence() (beers.sequence.sequence_by_synthesis_step.SequenceBySynthesisStep method)

read_starts (beers.cluster.Cluster attribute) read_strands (beers.cluster.Cluster attribute)

S

SAM (class in beers.sam) SecondStrandSynthesisStep (class in beers.library_prep.second_strand_synthesis_step) SequenceBySynthesisStep (class in beers.sequence.sequence_by_synthesis_step) SequencePipeline (class in beers.sequence.sequence_pipeline)

serialize() (beers.cluster.Cluster method) (beers.cluster_packet.ClusterPacket method) set_flowcell_coordinate_ranges() (beers.flowcell.Flowcell method) SizingStep (class in beers.library_prep.sizing_step)

V

validate() (beers.flowcell.Flowcell method) (beers.library_prep.library_prep_pipeline.LibraryPrepPipeline static method) (beers.library_prep.pcr_amplification_step.PCRAmplificationStep static method) (beers.sequence.sequence_pipeline.SequencePipeline static method)