Index

A

adaptive_bins_arm() (in module hatchet.utils.combine_counts) addchr() (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) addchrplt() (in module hatchet.utils.plot_cn) AlleleCounter (class in hatchet.utils.count_alleles) allelicprofiles() (in module hatchet.utils.plot_cn) allelicproportions() (in module hatchet.utils.plot_cn) apply_EM() (in module hatchet.utils.combine_counts)

argmax() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) (in module hatchet.utils.Supporting) argmin() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) (in module hatchet.utils.Supporting)

B

backtrack() (in module hatchet.utils.combine_counts) backward() (in module hatchet.bin.HATCHet) baf() (in module hatchet.utils.plot_bins) base (hatchet.utils.solve.ilp_subset.ILPSubset property) bb() (in module hatchet.utils.plot_bins) BBLUE (hatchet.utils.Supporting.bcolors attribute) bcolors (class in hatchet.utils.Supporting) biallelic() (hatchet.utils.phase_snps.Phaser method) bin() (in module hatchet.utils.BAMBinning)

binChr() (hatchet.utils.BAMBinning.Binner method) (hatchet.utils.TotalCounting.TotalCounter method) (in module hatchet.utils.CoordinateFinding) Binner (class in hatchet.utils.BAMBinning) binom_prop_test() (in module hatchet.utils.combine_counts) block_segment() (in module hatchet.utils.combine_counts) blocking() (in module hatchet.utils.combine_counts_fw) BOLD (hatchet.utils.Supporting.bcolors attribute) build_random_u() (hatchet.utils.solve.ilp_subset.ILPSubset method) build_symmetry_breaking() (hatchet.utils.solve.ilp_subset.ILPSubset method)

C

call() (in module hatchet.utils.genotype_snps) Caller (class in hatchet.utils.genotype_snps) callSNPs() (hatchet.utils.genotype_snps.Caller method) central() (in module hatchet.bin.HATCHet) change_chr() (hatchet.utils.phase_snps.Phaser method) check_array_files() (in module hatchet.utils.count_reads) check_counts_files() (in module hatchet.utils.count_reads) checkShift() (in module hatchet.utils.count_alleles) checksum() (in module hatchet.utils.Supporting) cleanup() (in module hatchet.utils.phase_snps) close() (in module hatchet.utils.Supporting) clubaf() (in module hatchet.utils.plot_bins) clurdr() (in module hatchet.utils.plot_bins) clus() (in module hatchet.utils.plot_bins) cluster() (in module hatchet.utils.cluster_bins_gmm) cluster_bins() (in module hatchet.utils.plot_bins) cn2evs() (in module hatchet.utils.plot_cn_1d2d) cn2total() (in module hatchet.utils.plot_cn_1d2d) cn2totals() (in module hatchet.utils.plot_cn_1d2d) cndistance() (in module hatchet.utils.plot_cn) cnproportions() (in module hatchet.utils.plot_cn)

collapse_blocks() (in module hatchet.utils.combine_counts) combine() (in module hatchet.utils.combine_counts_fw) compute_baf_task_multi() (in module hatchet.utils.combine_counts) compute_baf_task_single() (in module hatchet.utils.combine_counts) compute_baf_wrapper() (in module hatchet.utils.combine_counts) compute_gamma() (in module hatchet.utils.plot_cn_1d2d) computeBAFs() (in module hatchet.utils.combine_counts_fw) computeSizes() (in module hatchet.bin.HATCHet) concat() (in module hatchet.utils.phase_snps) Config (class in hatchet.utils.config) ConfigSection (class in hatchet.utils.config) consecutive() (in module hatchet.utils.combine_counts) CoordinateDescent (class in hatchet.utils.solve.cd) CoordinateDescentSplit (class in hatchet.utils.solve.cd) coordinates() (in module hatchet.utils.plot_bins) correct_haplotypes() (in module hatchet.utils.combine_counts) count_chromosome() (in module hatchet.utils.count_reads) count_chromosome_wrapper() (in module hatchet.utils.count_reads) countAlleles() (hatchet.utils.count_alleles.AlleleCounter method) counting() (in module hatchet.utils.count_alleles) create_model() (hatchet.utils.solve.ilp_subset.ILPSubset method) (hatchet.utils.solve.ilp_subset.ILPSubsetSplit method)

D

debug() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) DiagGHMM (class in hatchet.utils.cluster_bins)

digits() (in module hatchet.utils.Supporting) download() (in module hatchet.utils.Supporting) dwnld_chains() (in module hatchet.utils.download_panel) dwnld_refpanel_genome() (in module hatchet.utils.download_panel)

E

EM() (in module hatchet.utils.combine_counts) ENDC (hatchet.utils.Supporting.bcolors attribute) ensure() (in module hatchet.utils.Supporting) error() (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) (in module hatchet.utils.Supporting)

estimate_forward() (in module hatchet.bin.HATCHet) execute() (in module hatchet.bin.HATCHet) execute_python() (in module hatchet.bin.HATCHet) expected_arrays() (in module hatchet.utils.count_reads) expected_counts_files() (in module hatchet.utils.count_reads) extractChr() (in module hatchet.utils.CoordinateFinding) extractChromosomes() (in module hatchet.utils.ArgParsing)

F

FAIL (hatchet.utils.Supporting.bcolors attribute) filtering() (in module hatchet.bin.HATCHet) findClonalClusters() (in module hatchet.bin.HATCHet) findEnd() (in module hatchet.utils.CoordinateFinding) findNeutralCluster() (in module hatchet.bin.HATCHet) findStart() (in module hatchet.utils.CoordinateFinding) first_hot_start() (hatchet.utils.solve.ilp_subset.ILPSubset method)

fix_c() (hatchet.utils.solve.ilp_subset.ILPSubset method) fix_given_cn() (hatchet.utils.solve.ilp_subset.ILPSubset method) fix_u() (hatchet.utils.solve.ilp_subset.ILPSubset method) form_counts_array() (in module hatchet.utils.count_reads) form_seg() (in module hatchet.utils.cluster_bins) form_transition_matrix() (hatchet.utils.cluster_bins.DiagGHMM method) forward() (in module hatchet.bin.HATCHet)

G

generate_1D2D_plots() (in module hatchet.utils.plot_cn_1d2d) generateClouds() (in module hatchet.utils.cluster_bins_gmm) get_chr_end() (in module hatchet.utils.combine_counts) (in module hatchet.utils.count_reads)

getPoints() (in module hatchet.utils.cluster_bins_gmm) getSQNames() (in module hatchet.utils.ArgParsing) gridmixtures() (in module hatchet.utils.plot_cn) gridprofiles() (in module hatchet.utils.plot_cn) gridprofilesreduced() (in module hatchet.utils.plot_cn)

H

hatchet module hatchet.bin module hatchet.bin.HATCHet module hatchet.data module hatchet.utils module hatchet.utils.ArgParsing module hatchet.utils.BAMBinning module hatchet.utils.check module hatchet.utils.check_solver module hatchet.utils.cluster_bins module hatchet.utils.cluster_bins_gmm module hatchet.utils.combine_counts module hatchet.utils.combine_counts_fw module hatchet.utils.commands module hatchet.utils.config module hatchet.utils.CoordinateFinding module hatchet.utils.count_alleles module hatchet.utils.count_reads module hatchet.utils.count_reads_fw module

hatchet.utils.download_panel module hatchet.utils.genotype_snps module hatchet.utils.multiprocessing module hatchet.utils.phase_snps module hatchet.utils.plot_bins module hatchet.utils.plot_bins_1d2d module hatchet.utils.plot_cn module hatchet.utils.plot_cn_1d2d module hatchet.utils.ProgressBar module hatchet.utils.rd_gccorrect module hatchet.utils.run module hatchet.utils.solve module hatchet.utils.solve.cd module hatchet.utils.solve.ilp_subset module hatchet.utils.solve.utils module hatchet.utils.Supporting module hatchet.utils.TotalCounting module HEADER (hatchet.utils.Supporting.bcolors attribute) hmm_model_select() (in module hatchet.utils.cluster_bins) hot_start() (hatchet.utils.solve.ilp_subset.ILPSubset method)

I

ILPSubset (class in hatchet.utils.solve.ilp_subset) ILPSubsetSplit (class in hatchet.utils.solve.ilp_subset) index() (hatchet.utils.phase_snps.Phaser method) info() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) init_from_files() (hatchet.utils.config.Config method) intergridfullprofiles() (in module hatchet.utils.plot_cn) intergridreducedprofiles() (in module hatchet.utils.plot_cn)

intergridsamplesclusters() (in module hatchet.utils.plot_cn) intergridsubclonality() (in module hatchet.utils.plot_cn) interjoin() (in module hatchet.utils.plot_cn) interreduction() (in module hatchet.utils.plot_cn) isfloat() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) isHet() (in module hatchet.utils.count_alleles) items() (hatchet.utils.config.ConfigSection method)

J

join() (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn)

K

knownRegions() (in module hatchet.utils.count_reads_fw)

L

liftover() (hatchet.utils.phase_snps.Phaser method) limits_valid() (in module hatchet.utils.plot_cn_1d2d) log() (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) (in module hatchet.utils.Supporting)

logArgs() (in module hatchet.bin.HATCHet) (in module hatchet.utils.count_reads_fw) (in module hatchet.utils.Supporting)

M

M (hatchet.utils.solve.ilp_subset.ILPSubset property) main() (in module hatchet.bin.HATCHet) (in module hatchet.utils.check) (in module hatchet.utils.check_solver) (in module hatchet.utils.cluster_bins) (in module hatchet.utils.cluster_bins_gmm) (in module hatchet.utils.combine_counts) (in module hatchet.utils.combine_counts_fw) (in module hatchet.utils.count_alleles) (in module hatchet.utils.count_reads) (in module hatchet.utils.count_reads_fw) (in module hatchet.utils.download_panel) (in module hatchet.utils.genotype_snps) (in module hatchet.utils.phase_snps) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_bins_1d2d) (in module hatchet.utils.plot_cn) (in module hatchet.utils.plot_cn_1d2d) (in module hatchet.utils.run) make_transmat() (in module hatchet.utils.cluster_bins) makeBaseCMD() (in module hatchet.bin.HATCHet) merge_data() (in module hatchet.utils.combine_counts) merge_phasing() (in module hatchet.utils.combine_counts) minSegmentBins() (in module hatchet.utils.cluster_bins_gmm) mk_rename_file() (in module hatchet.utils.download_panel) module hatchet hatchet.bin hatchet.bin.HATCHet hatchet.data hatchet.utils hatchet.utils.ArgParsing hatchet.utils.BAMBinning hatchet.utils.check hatchet.utils.check_solver hatchet.utils.cluster_bins hatchet.utils.cluster_bins_gmm hatchet.utils.combine_counts hatchet.utils.combine_counts_fw hatchet.utils.commands hatchet.utils.config hatchet.utils.CoordinateFinding hatchet.utils.count_alleles hatchet.utils.count_reads hatchet.utils.count_reads_fw hatchet.utils.download_panel hatchet.utils.genotype_snps hatchet.utils.multiprocessing hatchet.utils.phase_snps hatchet.utils.plot_bins hatchet.utils.plot_bins_1d2d hatchet.utils.plot_cn hatchet.utils.plot_cn_1d2d hatchet.utils.ProgressBar hatchet.utils.rd_gccorrect hatchet.utils.run hatchet.utils.solve hatchet.utils.solve.cd hatchet.utils.solve.ilp_subset hatchet.utils.solve.utils hatchet.utils.Supporting hatchet.utils.TotalCounting

mosdepth_wrapper() (in module hatchet.utils.count_reads) multiple() (in module hatchet.utils.plot_cn) multisample_em() (in module hatchet.utils.combine_counts)

N

naturalOrder() (in module hatchet.utils.Supporting)

numericOrder() (in module hatchet.utils.Supporting)

O

OKBLUE (hatchet.utils.Supporting.bcolors attribute) OKGREEN (hatchet.utils.Supporting.bcolors attribute)

optimized_cA (hatchet.utils.solve.ilp_subset.ILPSubset property) optimized_cB (hatchet.utils.solve.ilp_subset.ILPSubset property) optimized_u (hatchet.utils.solve.ilp_subset.ILPSubset property)

P

parse_clonal() (in module hatchet.utils.solve.utils) parse_clonal_diploid() (in module hatchet.bin.HATCHet) parse_clonal_tetraploid() (in module hatchet.bin.HATCHet) parse_cluster_bins_args() (in module hatchet.utils.ArgParsing) parse_cluster_bins_gmm_args() (in module hatchet.utils.ArgParsing) parse_combine_counts_args() (in module hatchet.utils.ArgParsing) parse_combine_counts_fw_args() (in module hatchet.utils.ArgParsing) parse_count_alleles_arguments() (in module hatchet.utils.ArgParsing) parse_count_reads_args() (in module hatchet.utils.ArgParsing) parse_count_reads_fw_arguments() (in module hatchet.utils.ArgParsing) parse_download_panel_arguments() (in module hatchet.utils.ArgParsing) parse_genotype_snps_arguments() (in module hatchet.utils.ArgParsing) parse_phase_snps_arguments() (in module hatchet.utils.ArgParsing) parse_plot_bins_1d2d_args() (in module hatchet.utils.ArgParsing) parse_plot_bins_args() (in module hatchet.utils.ArgParsing) parse_plot_cn_1d2d_args() (in module hatchet.utils.ArgParsing) parseClonalClusters() (in module hatchet.bin.HATCHet) parseRegions() (in module hatchet.utils.ArgParsing)

parsing_arguments() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_cn) phase_blocks_sequential() (in module hatchet.utils.combine_counts) Phaser (class in hatchet.utils.phase_snps) plot_1d() (in module hatchet.utils.plot_bins_1d2d) plot_2d() (in module hatchet.utils.plot_bins_1d2d) plot_clusters() (in module hatchet.utils.plot_cn_1d2d) plot_genome() (in module hatchet.utils.plot_cn_1d2d) plot_track() (in module hatchet.utils.plot_bins_1d2d) pp() (in module hatchet.utils.plot_cn) print_log() (in module hatchet.utils.phase_snps) profiles() (in module hatchet.utils.plot_cn) progress() (hatchet.bin.HATCHet.ProgressBar method) (hatchet.utils.ProgressBar.ProgressBar method) ProgressBar (class in hatchet.bin.HATCHet) (class in hatchet.utils.ProgressBar) progressLock() (hatchet.utils.ProgressBar.ProgressBar method) progressNoLock() (hatchet.utils.ProgressBar.ProgressBar method)

R

Random (class in hatchet.utils.solve.utils) rd_gccorrect() (in module hatchet.utils.rd_gccorrect) rdr() (in module hatchet.utils.plot_bins) read() (hatchet.utils.config.Config method) read_bb() (in module hatchet.utils.cluster_bins) read_snps() (in module hatchet.utils.combine_counts) (in module hatchet.utils.count_reads) readBAFs() (in module hatchet.utils.combine_counts_fw) readBB() (in module hatchet.utils.cluster_bins_gmm) readBBC() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) readBINs() (in module hatchet.utils.combine_counts_fw) readPhase() (in module hatchet.utils.combine_counts_fw) readSEG() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) readTotalCounts() (in module hatchet.utils.combine_counts_fw) readUCN() (in module hatchet.utils.plot_cn) recompose_state() (in module hatchet.utils.plot_cn_1d2d) reduction() (in module hatchet.utils.plot_cn) refineClustering() (in module hatchet.utils.cluster_bins_gmm)

reindex() (in module hatchet.utils.cluster_bins) (in module hatchet.utils.cluster_bins_gmm) (in module hatchet.utils.plot_cn_1d2d) roundAlphasBetas() (in module hatchet.utils.cluster_bins_gmm) run() (hatchet.utils.BAMBinning.Binner method) (hatchet.utils.genotype_snps.Caller method) (hatchet.utils.multiprocessing.TaskHandler method) (hatchet.utils.multiprocessing.Worker method) (hatchet.utils.solve.cd.CoordinateDescent method) (hatchet.utils.solve.cd.Worker method) (hatchet.utils.solve.ilp_subset.ILPSubset method) (hatchet.utils.TotalCounting.TotalCounter method) (in module hatchet.utils.Supporting) run_chromosome() (in module hatchet.utils.combine_counts) (in module hatchet.utils.count_reads) run_chromosome_wrapper() (in module hatchet.utils.combine_counts) (in module hatchet.utils.count_reads) run_mosdepth() (in module hatchet.utils.count_reads) run_shapeit() (hatchet.utils.phase_snps.Phaser method) runningDiploid() (in module hatchet.bin.HATCHet) runningTetraploid() (in module hatchet.bin.HATCHet)

S

safediv() (in module hatchet.bin.HATCHet) scale_rdr() (in module hatchet.utils.solve.utils) scaleBAF() (in module hatchet.utils.cluster_bins_gmm) sections() (hatchet.utils.config.Config method) segmentation() (in module hatchet.utils.solve.utils) segmentBins() (in module hatchet.utils.cluster_bins_gmm) segmented_piecewise() (in module hatchet.utils.combine_counts) segmenting() (in module hatchet.utils.plot_cn) select() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) selectDiploid() (in module hatchet.bin.HATCHet) selectHetSNPs() (in module hatchet.utils.count_alleles) selectTetraploid() (in module hatchet.bin.HATCHet) set_fit_request() (hatchet.utils.cluster_bins.DiagGHMM method) set_predict_proba_request() (hatchet.utils.cluster_bins.DiagGHMM method) set_predict_request() (hatchet.utils.cluster_bins.DiagGHMM method)

set_score_request() (hatchet.utils.cluster_bins.DiagGHMM method) similarity() (in module hatchet.utils.plot_cn) similaritysample() (in module hatchet.utils.plot_cn) single() (in module hatchet.utils.plot_cn) solve() (in module hatchet.utils.solve) solver_available() (in module hatchet.utils.solve) sortchr() (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) splitBAF() (in module hatchet.utils.cluster_bins_gmm) (in module hatchet.utils.combine_counts_fw) stage_vcfs() (hatchet.utils.phase_snps.Phaser method) str2cn() (in module hatchet.utils.plot_cn_1d2d) str2state() (in module hatchet.utils.plot_cn_1d2d) subclonal() (in module hatchet.utils.plot_cn) suppress_stdout() (in module hatchet.utils.check) symmCoeff() (hatchet.utils.solve.ilp_subset.ILPSubset static method)

T

t2s() (in module hatchet.bin.HATCHet) TaskHandler (class in hatchet.utils.multiprocessing)

tcount() (in module hatchet.utils.TotalCounting) to_tuple() (in module hatchet.utils.Supporting) TotalCounter (class in hatchet.utils.TotalCounting)

U

UNDERLINE (hatchet.utils.Supporting.bcolors attribute)

url_exists() (in module hatchet.utils.Supporting)

W

WARNING (hatchet.utils.Supporting.bcolors attribute) warning() (in module hatchet.bin.HATCHet) (in module hatchet.utils.plot_bins) (in module hatchet.utils.plot_cn) which() (in module hatchet.utils.Supporting)

work() (hatchet.utils.count_alleles.AlleleCounter method) (hatchet.utils.multiprocessing.Worker method) (hatchet.utils.phase_snps.Phaser method) Worker (class in hatchet.utils.multiprocessing) (class in hatchet.utils.solve.cd)