Index

A

assign_multimapped_reads() (src.coptr.bam_processor.BamProcessor method)

assign_reads() (src.coptr.read_assigner.ReadAssigner method)

B

BamProcessor (class in src.coptr.bam_processor)

bin_reads() (src.coptr.bam_processor.CoverageMapContig method) (src.coptr.coptr_ref.ReadFilterRef method)

C

check_add_mapping() (src.coptr.bam_processor.ReadContainer method) compute_bin_bounds() (src.coptr.coptr_ref.ReadFilterRef method) compute_bin_coverage() (src.coptr.bam_processor.BamProcessor method) compute_bin_size() (src.coptr.bam_processor.CoverageMapContig method) (src.coptr.coptr_ref.ReadFilterRef method) compute_elbo() (src.coptr.read_assigner.ReadAssigner method) compute_genomewide_bounds() (src.coptr.coptr_contig.CoPTRContig method) (src.coptr.coptr_ref.ReadFilterRef method) compute_log_likelihood() (src.coptr.coptr_contig.CoPTRContig method) (src.coptr.coptr_ref.CoPTRRef method)

compute_rolling_sum() (src.coptr.coptr_ref.ReadFilterRef method) construct_coverage_matrix() (src.coptr.coptr_contig.CoPTRContig method) CoPTRContig (class in src.coptr.coptr_contig) CoPTRContigEstimate (class in src.coptr.coptr_contig) CoPTRRef (class in src.coptr.coptr_ref) CoPTRRefEstimate (class in src.coptr.coptr_ref) count_reads() (src.coptr.bam_processor.CoverageMapContig method) (src.coptr.bam_processor.CoverageMapRef method) CoverageMap (class in src.coptr.bam_processor) CoverageMapContig (class in src.coptr.bam_processor) CoverageMapRef (class in src.coptr.bam_processor)

E

estimate_ptr() (src.coptr.coptr_ref.CoPTRRef method) estimate_ptr_maximum_likelihood() (src.coptr.coptr_contig.CoPTRContig method) estimate_ptrs() (src.coptr.coptr_contig.CoPTRContig method) (src.coptr.coptr_ref.CoPTRRef method)

estimate_ptrs_coptr_contig() (in module src.coptr.coptr_contig) estimate_ptrs_coptr_ref() (in module src.coptr.coptr_ref) estimate_slope_intercept() (src.coptr.coptr_contig.CoPTRContig method) extract_reads() (src.coptr.bam_processor.BamProcessor method)

F

filter_reads() (src.coptr.coptr_ref.ReadFilterRef method)

filter_reads_phase1() (src.coptr.coptr_ref.ReadFilterRef method) filter_reads_phase2() (src.coptr.coptr_ref.ReadFilterRef method)

G

get_fastq_name() (in module src.coptr.util) get_length() (src.coptr.bam_processor.CoverageMapContig method) (src.coptr.bam_processor.CoverageMapRef method) get_mappings() (src.coptr.bam_processor.ReadContainer method)

get_reads() (src.coptr.bam_processor.CoverageMapContig method) (src.coptr.bam_processor.CoverageMapRef method) get_ref_names() (src.coptr.bam_processor.BamProcessor method) get_ref_seq_lengths() (src.coptr.bam_processor.BamProcessor method) grad_W() (src.coptr.poisson_pca.PoissonPCA method)

I

index() (src.coptr.read_mapper.ReadMapper method)

L

log_likelihood() (src.coptr.poisson_pca.PoissonPCA method)

M

map() (src.coptr.read_mapper.ReadMapper method) merge() (src.coptr.bam_processor.BamProcessor method) module src.coptr.bam_processor src.coptr.coptr_contig src.coptr.coptr_ref src.coptr.poisson_pca src.coptr.read_assigner src.coptr.read_mapper src.coptr.util

P

passed_qc() (src.coptr.bam_processor.CoverageMapContig method) pca() (src.coptr.poisson_pca.PoissonPCA method)

PoissonPCA (class in src.coptr.poisson_pca) process_bam() (src.coptr.bam_processor.BamProcessor method)

Q

QCResult (class in src.coptr.coptr_ref)

quality_check() (src.coptr.coptr_ref.ReadFilterRef method)

R

ReadAssigner (class in src.coptr.read_assigner) ReadContainer (class in src.coptr.bam_processor) ReadFilterRef (class in src.coptr.coptr_ref)

ReadMapper (class in src.coptr.read_mapper) remove_reads_by_region() (src.coptr.coptr_ref.ReadFilterRef method) run_vi() (src.coptr.read_assigner.ReadAssigner method)

S

src.coptr.bam_processor module src.coptr.coptr_contig module src.coptr.coptr_ref module src.coptr.poisson_pca module

src.coptr.read_assigner module src.coptr.read_mapper module src.coptr.util module

U

update_eta() (src.coptr.read_assigner.ReadAssigner method) update_ori_ter() (src.coptr.coptr_ref.CoPTRRef method) update_phi() (src.coptr.read_assigner.ReadAssigner method)

update_ptrs() (src.coptr.coptr_ref.CoPTRRef method) update_V() (src.coptr.poisson_pca.PoissonPCA method) update_W() (src.coptr.poisson_pca.PoissonPCA method)