Index

_

__getitem__() (kbbq.covariate.Covariate method) (kbbq.read.ReadData method) __init__() (kbbq.covariate.Covariate method) (kbbq.covariate.CovariateData method) (kbbq.covariate.CycleCovariate method) (kbbq.covariate.DinucCovariate method) (kbbq.covariate.QCovariate method) (kbbq.covariate.RGCovariate method) (kbbq.read.ReadData method) (kbbq.recaltable.GATKReport method) (kbbq.recaltable.GATKTable method) (kbbq.recaltable.RecalibrationReport method)

__len__() (kbbq.read.ReadData method) __setitem__() (kbbq.covariate.Covariate method) (kbbq.read.ReadData method) __str__() (kbbq.covariate.Covariate method) (kbbq.covariate.CovariateData method) (kbbq.covariate.QCovariate method) (kbbq.read.ReadData method) (kbbq.recaltable.GATKReport method) (kbbq.recaltable.GATKTable method) (kbbq.recaltable.RecalibrationReport method)

A

add_trusted_kmers() (in module kbbq.bloom)

B

bam_to_bqsr_covariates() (in module kbbq.gatk.bqsr) bam_to_report() (in module kbbq.gatk.bqsr) bamread_adaptor_boundary() (in module kbbq.gatk.bqsr) bamread_bqsr_cycle() (in module kbbq.gatk.bqsr) bamread_bqsr_dinuc() (in module kbbq.gatk.bqsr) bamread_cycle_covariates() (in module kbbq.gatk.applybqsr)

bamread_dinuc_covariates() (in module kbbq.gatk.applybqsr) bamread_get_oq() (in module kbbq.compare_reads) (in module kbbq.read) bamread_get_quals() (in module kbbq.read) benchmark() (in module kbbq.benchmark) benchmark_files() (in module kbbq.benchmark)

C

calculate_q() (in module kbbq.benchmark) calculate_thresholds() (in module kbbq.bloom) canonical_name() (kbbq.read.ReadData method) complement (kbbq.compare_reads.Dinucleotide attribute) consume_read() (kbbq.covariate.CovariateData method) (kbbq.covariate.QCovariate method) (kbbq.covariate.RGCovariate method)

correction_len() (in module kbbq.bloom) count_read() (in module kbbq.bloom) Covariate (class in kbbq.covariate) CovariateData (class in kbbq.covariate) create_empty_nodegraph() (in module kbbq.bloom) cycle (kbbq.gatk.applybqsr.ModelDQs attribute) cyclecov (kbbq.covariate.CovariateData attribute) CycleCovariate (class in kbbq.covariate)

D

data (kbbq.recaltable.GATKTable attribute) description (kbbq.recaltable.GATKTable attribute) dinuc (kbbq.gatk.applybqsr.ModelDQs attribute) dinuc_to_int (kbbq.compare_reads.Dinucleotide attribute)

dinuccov (kbbq.covariate.CovariateData attribute) DinucCovariate (class in kbbq.covariate) Dinucleotide (class in kbbq.compare_reads) dinucs (kbbq.compare_reads.Dinucleotide attribute)

E

errors (kbbq.covariate.Covariate attribute) (kbbq.read.ReadData attribute)

F

fastq_cycle_covariates() (in module kbbq.compare_reads) fastq_dinuc_covariates() (in module kbbq.compare_reads) fastq_infer_rg() (in module kbbq.compare_reads) fastq_infer_secondinpair() (in module kbbq.compare_reads) fill_read_errors() (in module kbbq.recalibrate) find_corrected_sites() (in module kbbq.recalibrate) find_covariates() (in module kbbq.recalibrate) find_longest_trusted_block() (in module kbbq.bloom)

find_read_errors() (in module kbbq.compare_reads) find_trusted_kmers() (in module kbbq.recalibrate) fix_one() (in module kbbq.bloom) fix_overcorrection() (in module kbbq.bloom) from_bamread() (kbbq.read.ReadData class method) from_fastq() (kbbq.read.ReadData class method) fromfile() (kbbq.recaltable.GATKReport class method) fromstring() (kbbq.recaltable.GATKTable class method)

G

gatk_delta_q() (in module kbbq.compare_reads) GATKReport (class in kbbq.recaltable) GATKTable (class in kbbq.recaltable) generate_reads_from_files() (in module kbbq.recalibrate) generic_cycle_covariate() (in module kbbq.compare_reads) generic_dinuc_covariate() (in module kbbq.compare_reads) get_bam_readname() (in module kbbq.benchmark) get_bed_dict() (in module kbbq.benchmark) get_colfmts() (kbbq.recaltable.GATKTable method) get_cycle_array() (kbbq.read.ReadData method) get_cycle_errors() (kbbq.read.ReadData method) get_datastring() (kbbq.recaltable.GATKTable method) get_delta_qs() (in module kbbq.gatk.applybqsr) get_dinuc_errors() (kbbq.read.ReadData method) get_dinucleotide_array() (kbbq.read.ReadData method) get_dqs_from_corrected() (in module kbbq.recalibrate) get_dqs_with_hashes() (in module kbbq.recalibrate) get_error_dict() (in module kbbq.benchmark) get_fastq_readname() (in module kbbq.benchmark) get_fmtstring() (kbbq.recaltable.GATKTable method)

get_full_skips() (in module kbbq.benchmark) get_headerstring() (kbbq.recaltable.GATKReport method) get_modeldqs_from_covariates() (in module kbbq.gatk.applybqsr) get_modelvecs_from_covariates() (in module kbbq.gatk.applybqsr) get_ncols() (kbbq.recaltable.GATKTable method) get_nrows() (kbbq.recaltable.GATKTable method) get_num_cycles() (kbbq.covariate.CovariateData method) get_num_dinucs() (kbbq.covariate.CovariateData method) get_num_qs() (kbbq.covariate.CovariateData method) get_num_rgs() (kbbq.covariate.CovariateData method) get_pu() (kbbq.read.ReadData method) get_q_errors() (kbbq.read.ReadData method) get_ref_dict() (in module kbbq.benchmark) get_rg_errors() (kbbq.read.ReadData method) get_rg_int() (kbbq.read.ReadData method) get_rg_to_pu() (in module kbbq.compare_reads) get_titlestring() (kbbq.recaltable.GATKTable method) get_unindexed() (kbbq.recaltable.GATKTable method) get_var_sites() (in module kbbq.benchmark) (in module kbbq.compare_reads)

I

i (kbbq.compare_reads.RescaledNormal attribute) increment() (kbbq.covariate.Covariate method)

infer_errors() (in module kbbq.bloom) infer_errors_from_trusted_kmers() (in module kbbq.bloom) infer_read_errors() (in module kbbq.bloom)

K

kbbq (module) kbbq.benchmark (module) kbbq.bloom (module) kbbq.compare_reads (module) kbbq.covariate (module) kbbq.gatk (module)

kbbq.gatk.applybqsr (module) kbbq.gatk.bqsr (module) kbbq.plot (module) kbbq.read (module) kbbq.recalibrate (module) kbbq.recaltable (module) kmers_in_graph() (in module kbbq.bloom)

L

load_headers_from_bams() (in module kbbq.recalibrate) load_positions() (in module kbbq.compare_reads)

load_rgs_from_bamfile() (kbbq.read.ReadData class method) load_subsampled_hash() (in module kbbq.recalibrate)

M

maxscore (kbbq.compare_reads.RescaledNormal attribute)

mean (kbbq.gatk.applybqsr.ModelDQs attribute) ModelDQs (class in kbbq.gatk.applybqsr)

N

name (kbbq.read.ReadData attribute) not_skipped_errors() (kbbq.read.ReadData method) nparray_to_qualitystring() (in module kbbq.compare_reads) nucleotides (kbbq.compare_reads.Dinucleotide attribute)

num_cycles() (kbbq.covariate.CycleCovariate method) num_dinucs() (kbbq.covariate.DinucCovariate method) num_qs() (kbbq.covariate.QCovariate method) num_rgs() (kbbq.covariate.RGCovariate method) numrgs (kbbq.read.ReadData attribute)

O

oldset (kbbq.compare_reads.RescaledNormal attribute) open_bedfile() (in module kbbq.benchmark) open_outputs() (in module kbbq.recalibrate)

opens_as_bam() (in module kbbq.recalibrate) overlapping_kmers_in_graph() (in module kbbq.bloom) overlapping_kmers_possible() (in module kbbq.bloom)

P

p_kmer_added() (in module kbbq.bloom) p_to_q() (in module kbbq.compare_reads) pad_axis() (in module kbbq.covariate) (kbbq.covariate.Covariate method) (kbbq.covariate.CycleCovariate method) pad_axis_to_fit() (kbbq.covariate.Covariate method) parse_fmtstring() (kbbq.recaltable.GATKTable static method)

plot_benchmark() (in module kbbq.plot) possible_diffs (kbbq.compare_reads.RescaledNormal attribute) precisionmap (kbbq.recaltable.GATKTable attribute) print_benchmark() (in module kbbq.benchmark) print_info() (in module kbbq.compare_reads) prior() (kbbq.compare_reads.RescaledNormal class method) prior_dist (kbbq.compare_reads.RescaledNormal attribute)

Q

q (kbbq.gatk.applybqsr.ModelDQs attribute) q_to_p() (in module kbbq.compare_reads) qcov (kbbq.covariate.CovariateData attribute)

QCovariate (class in kbbq.covariate) qual (kbbq.read.ReadData attribute) quantize() (in module kbbq.gatk.bqsr)

R

ReadData (class in kbbq.read) recalibrate() (in module kbbq.recalibrate) recalibrate_and_write() (in module kbbq.recalibrate) recalibrate_bamread() (in module kbbq.gatk.applybqsr) recalibrate_fastq() (in module kbbq.compare_reads) (in module kbbq.recalibrate) recalibrate_read() (in module kbbq.recalibrate) RecalibrationReport (class in kbbq.recaltable)

regression_recalibrate() (in module kbbq.compare_reads) RescaledNormal (class in kbbq.compare_reads) rg (kbbq.gatk.applybqsr.ModelDQs attribute) (kbbq.read.ReadData attribute) rg_to_int (kbbq.read.ReadData attribute) rg_to_pu (kbbq.read.ReadData attribute) rgcov (kbbq.covariate.QCovariate attribute) RGCovariate (class in kbbq.covariate) rolling_window() (in module kbbq.bloom)

S

second (kbbq.read.ReadData attribute) seq (kbbq.read.ReadData attribute)

shape (kbbq.covariate.Covariate attribute) skips (kbbq.read.ReadData attribute) str_qual() (kbbq.read.ReadData method)

T

table_to_vectors() (in module kbbq.gatk.applybqsr) tables (kbbq.recaltable.GATKReport attribute) title (kbbq.recaltable.GATKTable attribute) total (kbbq.covariate.Covariate attribute)

train_regression() (in module kbbq.compare_reads) trim_bamread() (in module kbbq.gatk.bqsr) tstamp() (in module kbbq.compare_reads) typemap (kbbq.recaltable.GATKTable attribute)

V

validate_files() (in module kbbq.recalibrate) veccomplement() (kbbq.compare_reads.Dinucleotide class method) vecget() (kbbq.compare_reads.Dinucleotide class method)

vectorized_complement (kbbq.compare_reads.Dinucleotide attribute) vectorized_get (kbbq.compare_reads.Dinucleotide attribute) vectors_to_report() (in module kbbq.gatk.bqsr) version (kbbq.recaltable.GATKReport attribute)

W

write() (kbbq.recaltable.GATKReport method) (kbbq.recaltable.GATKTable method)

Y

yield_reads() (in module kbbq.recalibrate)