Index

A

add() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) add_C() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) add_chrom_data() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) add_chrom_data_PV() (MACS3.Signal.BedGraph.bedGraphTrackI method) add_chromosome() (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) add_loc() (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.Region.Regions method) add_loc_wo_merge() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method)

add_PeakContent() (MACS3.IO.PeakIO.PeakIO method) add_T() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) add_to_unitig_list() (MACS3.Signal.RACollection.RACollection method) add_variant() (MACS3.Signal.PeakVariants.PeakVariants method) align_unitig_to_REFSEQ() (MACS3.Signal.RACollection.RACollection method) aln_length (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) alt_allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) alternative_d (MACS3.Signal.PeakModel.PeakModel attribute) annotation (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) apply_deltaBIC_cutoff() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) apply_func() (MACS3.Signal.BedGraph.bedGraphTrackI method) apply_GQ_cutoff() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) apply_multiple_cutoffs() (in module MACS3.Signal.CallPeakUnit) atof() (in module MACS3.IO.BedGraphIO) atoi() (in module MACS3.IO.BedGraphIO) average_template_length (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute)

B

bai_filename (MACS3.IO.BAM.BAMaccessor attribute) BAIFile (class in MACS3.IO.BAM) baifile (MACS3.IO.BAM.BAMaccessor attribute) bam_filename (MACS3.IO.BAM.BAMaccessor attribute) BAMaccessor (class in MACS3.IO.BAM) bamfile (MACS3.IO.BAM.BAMaccessor attribute) barcode_dict (MACS3.Signal.PairedEndTrack.PETrackII attribute) barcode_last_n (MACS3.Signal.PairedEndTrack.PETrackII attribute) barcodes (MACS3.Signal.PairedEndTrack.PETrackII attribute) baseline_value (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) bedGraph_control_filename (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) bedGraph_ctrl_f (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) bedGraph_filename (MACS3.IO.BedGraphIO.bedGraphIO attribute) bedGraph_filename_prefix (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) bedGraph_treat_f (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) bedGraph_treat_filename (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) bedGraphIO (class in MACS3.IO.BedGraphIO) bedGraphTrackI (class in MACS3.Signal.BedGraph) bedGraphTrackII (class in MACS3.Signal.BedGraph) bgzf_block_cache (MACS3.IO.BAM.BAMaccessor attribute) BIC_heter_AS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) BIC_heter_noAS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) BIC_homo_major (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) BIC_homo_minor (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) binaryqual (MACS3.Signal.ReadAlignment.ReadAlignment attribute) binaryseq (MACS3.Signal.ReadAlignment.ReadAlignment attribute) binomial_cdf() (in module MACS3.Signal.Prob) binomial_cdf_inv() (in module MACS3.Signal.Prob) binomial_coef() (in module MACS3.Signal.Prob) binomial_pdf() (in module MACS3.Signal.Prob) binomial_sf() (in module MACS3.Signal.Prob) bins (MACS3.IO.BAM.BAIFile attribute) blockNum (MACS3.IO.PeakIO.BroadPeakContent attribute) blockSizes (MACS3.IO.PeakIO.BroadPeakContent attribute)

blockStarts (MACS3.IO.PeakIO.BroadPeakContent attribute) bool() (in module MACS3.IO.BAM) (in module MACS3.IO.BedGraphIO) (in module MACS3.IO.PeakIO) (in module MACS3.Signal.BedGraph) (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.FixWidthTrack) (in module MACS3.Signal.PairedEndTrack) (in module MACS3.Signal.PeakModel) (in module MACS3.Signal.PeakVariants) (in module MACS3.Signal.Pileup) (in module MACS3.Signal.PosReadsInfo) (in module MACS3.Signal.Prob) (in module MACS3.Signal.RACollection) (in module MACS3.Signal.ReadAlignment) (in module MACS3.Signal.Region) (in module MACS3.Signal.ScoreTrack) (in module MACS3.Signal.SignalProcessing) (in module MACS3.Signal.UnitigRACollection) (in module MACS3.Signal.VariantStat) bq_set_C (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) bq_set_T (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) BroadPeakContent (class in MACS3.IO.PeakIO) BroadPeakIO (class in MACS3.IO.PeakIO) buf_size (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) buffer_size (MACS3.Signal.BedGraph.bedGraphTrackII attribute) (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) build() (MACS3.Signal.PeakModel.PeakModel method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) build_chromosome() (MACS3.Signal.ScoreTrack.TwoConditionScores method) build_unitig_collection() (MACS3.Signal.RACollection.RACollection method) bw (MACS3.Signal.PeakModel.PeakModel attribute)

C

c1bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) c2bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) c_quick_pileup() (in module MACS3.Signal.Pileup) c_single_end_pileup() (in module MACS3.Signal.Pileup) c_write_pv_array_to_bedGraph() (in module MACS3.Signal.Pileup) calculate_elbows() (in module MACS3.Signal.BedGraph) calculate_GQ() (in module MACS3.Signal.VariantStat) calculate_GQ_heterASsig() (in module MACS3.Signal.VariantStat) calculate_ln() (in module MACS3.Signal.VariantStat) call_broadpeaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) call_GT() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) call_peaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.PeakDetect.PeakDetect method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) CallerFromAlignments (class in MACS3.Signal.CallPeakUnit) CalModel_Heter_AS() (in module MACS3.Signal.VariantStat) CalModel_Heter_noAS() (in module MACS3.Signal.VariantStat) CalModel_Homo() (in module MACS3.Signal.VariantStat) change_normalization_method() (MACS3.Signal.ScoreTrack.ScoreTrackII method) change_score_method() (MACS3.Signal.ScoreTrack.ScoreTrackII method) chi2_k1_cdf() (in module MACS3.Signal.CallPeakUnit) chi2_k2_cdf() (in module MACS3.Signal.CallPeakUnit) chi2_k4_cdf() (in module MACS3.Signal.CallPeakUnit) chisq_logp_e() (in module MACS3.Signal.Prob) chisq_pvalue_e() (in module MACS3.Signal.Prob) chr_pos_treat_ctrl (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) chrom (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.Signal.PeakVariants.PeakVariants attribute) (MACS3.Signal.RACollection.RACollection attribute) (MACS3.Signal.ReadAlignment.ReadAlignment attribute) (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)

chromosomes (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) cigar (MACS3.Signal.ReadAlignment.ReadAlignment attribute) clean_up_ndarray() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.Pileup) (in module MACS3.Signal.PileupV2) close() (MACS3.IO.BAM.BAMaccessor method) CO_sorted (MACS3.IO.PeakIO.PeakIO attribute) coffset_cache (MACS3.IO.BAM.BAMaccessor attribute) compute_foldenrichment() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_likelihood() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_logFE() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_max() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_pvalue() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_qvalue() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_region_tags_from_peaks() (MACS3.Signal.FixWidthTrack.FWTrack method) compute_SPMR() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_subtraction() (MACS3.Signal.ScoreTrack.ScoreTrackII method) compute_sym_likelihood() (MACS3.Signal.ScoreTrack.ScoreTrackII method) cond1_factor (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) cond2_factor (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) converged (MACS3.Signal.HMMR_EM.HMMR_EM attribute) count_fraglengths() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) ctrl (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) ctrl_d_s (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) ctrl_edm (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) ctrl_scaling_factor_s (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) cutoff (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) cutoff_analysis() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) cutoff_analysis_filename (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)

D

d (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) (MACS3.Signal.PeakModel.PeakModel attribute) d_min (MACS3.Signal.PeakModel.PeakModel attribute) d_Variants (MACS3.Signal.PeakVariants.PeakVariants attribute) data (MACS3.IO.BedGraphIO.bedGraphIO attribute) (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) datalength (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)

debug (MACS3.Signal.PeakModel.PeakModel attribute) deltaBIC (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) destroy() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) diag_write() (in module MACS3.IO.OutputWriter) divide_func() (in module MACS3.Signal.BedGraph)

E

enable_trackline() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) end (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.Signal.PeakVariants.PeakVariants attribute) end_shift (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) enforce_peakyness() (in module MACS3.Signal.SignalProcessing) enforce_valleys() (in module MACS3.Signal.SignalProcessing) epsilon (MACS3.Signal.HMMR_EM.HMMR_EM attribute) erf() (in module MACS3.Signal.CallPeakUnit) error (MACS3.Signal.PeakModel.PeakModel attribute)

ex20() (in module MACS3.Signal.Prob) exclude() (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.Region.Regions method) exp() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.Prob) expand() (MACS3.Signal.Region.Regions method) extract_region_tags() (MACS3.Signal.FixWidthTrack.FWTrack method) extract_signals_from_regions() (in module MACS3.Signal.HMMR_Signal_Processing) extract_value() (MACS3.Signal.BedGraph.bedGraphTrackI method) extract_value_hmmr() (MACS3.Signal.BedGraph.bedGraphTrackI method)

F

factorial() (in module MACS3.Signal.Prob) fc (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) fclose() (in module MACS3.Signal.CallPeakUnit) fermi_assemble() (MACS3.Signal.RACollection.RACollection method) fermiNTs (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) fhd (MACS3.IO.BAM.BAIFile attribute) filename (MACS3.IO.BAM.BAIFile attribute) filter_dup() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) filter_fc() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) filter_pscore() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) filter_qscore() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) filter_score() (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) filter_unitig_with_bad_aln() (MACS3.Signal.RACollection.RACollection method) filterflag() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) filterout (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)

finalize() (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) find_optimal_cutoff() (in module MACS3.Signal.CallPeakUnit) fisher_func() (in module MACS3.Signal.BedGraph) fix_coordinates() (in module MACS3.Signal.Pileup) fix_indels() (MACS3.Signal.PeakVariants.PeakVariants method) float32_t() (in module MACS3.Signal.Prob) float64_t() (in module MACS3.Signal.Prob) fopen() (in module MACS3.Signal.CallPeakUnit) fprintf() (in module MACS3.Signal.CallPeakUnit) fraglengths() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) fragMeans (MACS3.Signal.HMMR_EM.HMMR_EM attribute) fragStddevs (MACS3.Signal.HMMR_EM.HMMR_EM attribute) fragVars (MACS3.Signal.HMMR_EM.HMMR_EM attribute) free() (in module MACS3.Signal.Pileup) (in module MACS3.Signal.RACollection) fw (MACS3.Signal.FixWidthTrack.FWTrack attribute) FWTrack (class in MACS3.Signal.FixWidthTrack)

G

generate_digested_signals() (in module MACS3.Signal.HMMR_Signal_Processing) generate_weight_mapping() (in module MACS3.Signal.HMMR_Signal_Processing) get_base_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_base_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_bins_by_region() (in module MACS3.IO.BAM) get_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_chr_names() (MACS3.IO.PeakIO.PeakIO method) (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.Region.Regions method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) get_chromosomes() (MACS3.IO.BAM.BAMaccessor method) get_chunks_by_bin() (MACS3.IO.BAM.BAIFile method) get_chunks_by_list_of_bins() (MACS3.IO.BAM.BAIFile method) get_chunks_by_list_of_regions() (MACS3.IO.BAM.BAIFile method) get_chunks_by_region() (MACS3.IO.BAM.BAIFile method) get_coffset_by_region() (MACS3.IO.BAM.BAIFile method) get_coffsets_by_list_of_regions() (MACS3.IO.BAM.BAIFile method) get_common_chrs() (MACS3.Signal.ScoreTrack.TwoConditionScores method) get_data_by_chr() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) get_data_from_chrom() (MACS3.IO.PeakIO.PeakIO method) get_FASTQ() (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.ReadAlignment.ReadAlignment method) get_from_multiple_scores() (in module MACS3.Signal.CallPeakUnit) get_locations_by_chr() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method)

get_logFE() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.ScoreTrack) get_logLR_asym() (in module MACS3.Signal.CallPeakUnit) get_memory_usage() (MACS3.Utilities.Logger.MemoryLogger static method) get_metadata_by_refseq() (MACS3.IO.BAM.BAIFile method) get_n_edits() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_PosReadsInfo_ref_pos() (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.UnitigRACollection.UnitigCollection method) get_pscore() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.ScoreTrack) get_reads_in_region() (MACS3.IO.BAM.BAMaccessor method) get_refer_biased_01s() (MACS3.Signal.PeakVariants.PeakVariants method) get_REFSEQ() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_rlengths() (MACS3.IO.BAM.BAMaccessor method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) get_subtraction() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.ScoreTrack) get_variant_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) (MACS3.Signal.UnitigRACollection.UnitigRAs method) get_weighted_density() (in module MACS3.Signal.HMMR_EM) (in module MACS3.Signal.HMMR_HMM) (in module MACS3.Signal.HMMR_Signal_Processing) getitem_then_subtract() (in module MACS3.Signal.CallPeakUnit) GQ (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) GQ_heter_AS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) GQ_heter_ASsig (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) GQ_heter_noAS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) GQ_homo_major (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) GreedyMaxFunctionAS() (in module MACS3.Signal.VariantStat) GreedyMaxFunctionNoAS() (in module MACS3.Signal.VariantStat) GT (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) gz (MACS3.Signal.PeakModel.PeakModel attribute)

H

hard_clip() (in module MACS3.Signal.SignalProcessing) has_indel() (MACS3.Signal.PeakVariants.PeakVariants method) has_refer_biased_01() (MACS3.Signal.PeakVariants.PeakVariants method) hasfermiinfor (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) heter_AS_alleleratio (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) heter_AS_kc (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) heter_AS_ki (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)

heter_noAS_kc (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) heter_noAS_ki (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) hmm_model_init() (in module MACS3.Signal.HMMR_HMM) hmm_model_save() (in module MACS3.Signal.HMMR_HMM) hmm_predict() (in module MACS3.Signal.HMMR_HMM) hmm_training() (in module MACS3.Signal.HMMR_HMM) HMMR_EM (class in MACS3.Signal.HMMR_EM)

I

info (MACS3.Signal.PeakModel.PeakModel attribute) init_from_PeakIO() (MACS3.Signal.Region.Regions method) int32_t() (in module MACS3.Signal.Prob) int64_t() (in module MACS3.Signal.Prob) int_max() (in module MACS3.Signal.ScoreTrack) int_min() (in module MACS3.Signal.ScoreTrack) internal_minima() (in module MACS3.Signal.SignalProcessing) intersect() (MACS3.Signal.Region.Regions method) is_destroyed (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute)

is_indel() (MACS3.Signal.PeakVariants.Variant method) is_only_del() (MACS3.Signal.PeakVariants.Variant method) is_only_insertion() (MACS3.Signal.PeakVariants.Variant method) is_refer_biased_01() (MACS3.Signal.PeakVariants.Variant method) is_sorted (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) is_valid_peak() (in module MACS3.Signal.SignalProcessing)

J

jump (MACS3.Signal.HMMR_EM.HMMR_EM attribute)

L

l (MACS3.Signal.ReadAlignment.ReadAlignment attribute) lambda_bg (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) left (MACS3.Signal.RACollection.RACollection attribute) (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) left_forward() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.FixWidthTrack) left_sum() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.FixWidthTrack) length (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) (MACS3.Signal.RACollection.RACollection attribute) (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) lmfold (MACS3.Signal.PeakModel.PeakModel attribute) lnL_heter_AS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) lnL_heter_noAS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) lnL_homo_major (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)

lnL_homo_minor (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) locations (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) log() (in module MACS3.Signal.Prob) (in module MACS3.Signal.ScoreTrack) log10() (in module MACS3.Signal.BedGraph) (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.ScoreTrack) log10_chi2_k1_cdf() (in module MACS3.Signal.CallPeakUnit) log10_chi2_k2_cdf() (in module MACS3.Signal.CallPeakUnit) log10_chi2_k4_CDF() (in module MACS3.Signal.CallPeakUnit) log10_poisson_cdf_P_large_lambda() (in module MACS3.Signal.Prob) log10_poisson_cdf_Q_large_lambda() (in module MACS3.Signal.Prob) log1p() (in module MACS3.Signal.CallPeakUnit) logLR_asym() (in module MACS3.Signal.ScoreTrack) logLR_sym() (in module MACS3.Signal.ScoreTrack) logspace_add() (in module MACS3.Signal.Prob) lpos (MACS3.Signal.ReadAlignment.ReadAlignment attribute) (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)

M

MACS3.Commands module MACS3.Commands.bdgbroadcall_cmd module MACS3.Commands.bdgdiff_cmd module MACS3.Commands.bdgpeakcall_cmd module MACS3.IO module MACS3.IO.BAM module MACS3.IO.BedGraphIO module MACS3.IO.OutputWriter module MACS3.IO.PeakIO module MACS3.Signal module MACS3.Signal.BedGraph module MACS3.Signal.CallPeakUnit module MACS3.Signal.FixWidthTrack module MACS3.Signal.HMMR_EM module MACS3.Signal.HMMR_HMM module MACS3.Signal.HMMR_Signal_Processing module MACS3.Signal.PairedEndTrack module MACS3.Signal.PeakDetect module MACS3.Signal.PeakModel module MACS3.Signal.PeakVariants module MACS3.Signal.Pileup module MACS3.Signal.PileupV2 module MACS3.Signal.PosReadsInfo module MACS3.Signal.Prob module MACS3.Signal.RACollection module MACS3.Signal.ReadAlignment module MACS3.Signal.Region module MACS3.Signal.ScoreTrack module MACS3.Signal.SignalProcessing module MACS3.Signal.UnitigRACollection module MACS3.Signal.VariantStat module MACS3.Utilities module MACS3.Utilities.Constants module MACS3.Utilities.Logger module

magic (MACS3.IO.BAM.BAIFile attribute) make_pq_table() (MACS3.Signal.ScoreTrack.ScoreTrackII method) make_PV_from_LR() (in module MACS3.Signal.PileupV2) make_PV_from_LRC() (in module MACS3.Signal.PileupV2) make_PV_from_PN() (in module MACS3.Signal.PileupV2) make_ScoreTrackII_for_macs() (MACS3.Signal.BedGraph.bedGraphTrackI method) malloc() (in module MACS3.Signal.RACollection) mapping_function_always_1() (in module MACS3.Signal.PileupV2) max_fraglen (MACS3.Signal.HMMR_EM.HMMR_EM attribute) max_pairnum (MACS3.Signal.PeakModel.PeakModel attribute) max_tags (MACS3.Signal.PeakModel.PeakModel attribute) maxima() (in module MACS3.Signal.SignalProcessing) maxIter (MACS3.Signal.HMMR_EM.HMMR_EM attribute) maxvalue (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) MD (MACS3.Signal.ReadAlignment.ReadAlignment attribute) MDTagMissingError mean() (in module MACS3.Signal.Pileup) mean_from_peakcontent() (MACS3.Signal.ScoreTrack.TwoConditionScores method) mean_from_value_length() (in module MACS3.Signal.CallPeakUnit) mean_func() (in module MACS3.Signal.BedGraph) median_from_value_length() (in module MACS3.Signal.CallPeakUnit) MemoryLogger (class in MACS3.Utilities.Logger) merge_overlap() (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.Region.Regions method) merge_regions() (MACS3.Signal.BedGraph.bedGraphTrackI method) metadata (MACS3.IO.BAM.BAIFile attribute) min_fraglen (MACS3.Signal.HMMR_EM.HMMR_EM attribute) min_tags (MACS3.Signal.PeakModel.PeakModel attribute) minus_line (MACS3.Signal.PeakModel.PeakModel attribute) minvalue (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) model2r_script() (in module MACS3.IO.OutputWriter) module MACS3.Commands MACS3.Commands.bdgbroadcall_cmd MACS3.Commands.bdgdiff_cmd MACS3.Commands.bdgpeakcall_cmd MACS3.IO MACS3.IO.BAM MACS3.IO.BedGraphIO MACS3.IO.OutputWriter MACS3.IO.PeakIO MACS3.Signal MACS3.Signal.BedGraph MACS3.Signal.CallPeakUnit MACS3.Signal.FixWidthTrack MACS3.Signal.HMMR_EM MACS3.Signal.HMMR_HMM MACS3.Signal.HMMR_Signal_Processing MACS3.Signal.PairedEndTrack MACS3.Signal.PeakDetect MACS3.Signal.PeakModel MACS3.Signal.PeakVariants MACS3.Signal.Pileup MACS3.Signal.PileupV2 MACS3.Signal.PosReadsInfo MACS3.Signal.Prob MACS3.Signal.RACollection MACS3.Signal.ReadAlignment MACS3.Signal.Region MACS3.Signal.ScoreTrack MACS3.Signal.SignalProcessing MACS3.Signal.UnitigRACollection MACS3.Signal.VariantStat MACS3.Utilities MACS3.Utilities.Constants MACS3.Utilities.Logger mutation_type (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)

N

n_bins (MACS3.IO.BAM.BAIFile attribute) n_chunks (MACS3.IO.BAM.BAIFile attribute) n_edits (MACS3.Signal.ReadAlignment.ReadAlignment attribute) n_edits_sum() (MACS3.Signal.RACollection.RACollection method) n_mapped (MACS3.IO.BAM.BAIFile attribute) n_reads (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) n_reads_C (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) n_reads_T (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) n_ref (MACS3.IO.BAM.BAIFile attribute) n_strand (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) n_tips (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)

n_unmapped (MACS3.IO.BAM.BAIFile attribute) n_variants() (MACS3.Signal.PeakVariants.PeakVariants method) naive_call_peaks() (in module MACS3.Signal.Pileup) naive_quick_pileup() (in module MACS3.Signal.Pileup) name (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.IO.PeakIO.PeakIO attribute) no_lambda_flag (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) noffset_cache (MACS3.IO.BAM.BAMaccessor attribute) normalization_method (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) normalize() (MACS3.Signal.ScoreTrack.ScoreTrackII method) NotEnoughPairsException

O

online_update() (in module MACS3.Signal.HMMR_EM) optimal_p_cutoff (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)

over_two_pv_array() (in module MACS3.Signal.Pileup) overlie() (MACS3.Signal.BedGraph.bedGraphTrackI method)

P

p2q() (MACS3.Signal.BedGraph.bedGraphTrackI method) pduplication() (in module MACS3.Signal.Prob) PE_mode (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) peak (MACS3.Signal.RACollection.RACollection attribute) (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) peak_refseq (MACS3.Signal.RACollection.RACollection attribute) peak_refseq_ext (MACS3.Signal.RACollection.RACollection attribute) PeakContent (class in MACS3.IO.PeakIO) PeakDetect (class in MACS3.Signal.PeakDetect) PeakIO (class in MACS3.IO.PeakIO) PeakModel (class in MACS3.Signal.PeakModel) peaks (MACS3.IO.PeakIO.BroadPeakIO attribute) (MACS3.IO.PeakIO.PeakIO attribute) peaksize (MACS3.Signal.PeakModel.PeakModel attribute) PeakVariants (class in MACS3.Signal.PeakVariants) PETrackI (class in MACS3.Signal.PairedEndTrack) PETrackII (class in MACS3.Signal.PairedEndTrack) pileup (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) pileup_a_chromosome() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_a_chromosome_c() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_and_write_pe() (in module MACS3.Signal.Pileup) pileup_and_write_se() (in module MACS3.Signal.Pileup) pileup_bdg() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_bdg2() (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_bdg_hmmr() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_data_files (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) pileup_from_LR() (in module MACS3.Signal.PileupV2) pileup_from_LR_hmmratac() (in module MACS3.Signal.PileupV2)

pileup_from_LRC() (in module MACS3.Signal.PileupV2) pileup_from_PN() (in module MACS3.Signal.PileupV2) pileup_PV() (in module MACS3.Signal.PileupV2) pileup_treat_ctrl_a_chromosome() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) PL_00 (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) PL_01 (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) PL_11 (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) plus_line (MACS3.Signal.PeakModel.PeakModel attribute) pnorm() (in module MACS3.Signal.Prob) pnorm2() (in module MACS3.Signal.Prob) pointer (MACS3.Signal.FixWidthTrack.FWTrack attribute) poisson_cdf() (in module MACS3.Signal.Prob) poisson_cdf_inv() (in module MACS3.Signal.Prob) poisson_cdf_Q_inv() (in module MACS3.Signal.Prob) poisson_pdf() (in module MACS3.Signal.Prob) pop() (MACS3.Signal.Region.Regions method) PosReadsInfo (class in MACS3.Signal.PosReadsInfo) PosVal() (in module MACS3.Signal.Pileup) poz() (in module MACS3.Signal.Prob) pqtable (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) print_to_bed() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) product_func() (in module MACS3.Signal.BedGraph) pscore (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) pseudocount (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) pvalue_all_done (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) pvalue_length (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) pvalue_npeaks (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) pvalue_stat (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) pvalue_stat1 (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) pvalue_stat2 (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) pvalue_stat3 (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)

Q

qscore (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute)

QUAL (MACS3.Signal.ReadAlignment.ReadAlignment attribute) quick_pileup() (in module MACS3.Signal.Pileup)

R

RACollection (class in MACS3.Signal.RACollection) RAlists (MACS3.Signal.RACollection.RACollection attribute) (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) randomly_pick() (MACS3.IO.PeakIO.PeakIO method) RAs_left (MACS3.Signal.RACollection.RACollection attribute) RAs_right (MACS3.Signal.RACollection.RACollection attribute) raw_read_depth() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) read_bedGraph() (MACS3.IO.BedGraphIO.bedGraphIO method) read_from_xls() (MACS3.IO.PeakIO.PeakIO method) ReadAlignment (class in MACS3.Signal.ReadAlignment) readname (MACS3.Signal.ReadAlignment.ReadAlignment attribute) ref_allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) ref_pos (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) reference_aln (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) reference_length (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) references (MACS3.IO.BAM.BAMaccessor attribute) refine_peaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) refseq (MACS3.Signal.PeakVariants.PeakVariants attribute) reg2bins() (in module MACS3.IO.BAM) RegionIO (class in MACS3.IO.PeakIO) Regions (class in MACS3.Signal.Region) regions (MACS3.IO.PeakIO.RegionIO attribute) (MACS3.Signal.Region.Regions attribute)

relative_ref_pos_to_relative_query_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) remap_RAs_w_unitigs() (MACS3.Signal.RACollection.RACollection method) remove_outliers() (MACS3.Signal.RACollection.RACollection method) remove_variant() (MACS3.Signal.PeakVariants.PeakVariants method) replace_variant() (MACS3.Signal.PeakVariants.PeakVariants method) reset_baseline() (MACS3.Signal.BedGraph.bedGraphTrackI method) return_greater() (in module MACS3.Signal.HMMR_EM) right (MACS3.Signal.RACollection.RACollection attribute) (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) right_forward() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.FixWidthTrack) right_sum() (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.FixWidthTrack) rlengths (MACS3.IO.BAM.BAMaccessor attribute) (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) rpos (MACS3.Signal.ReadAlignment.ReadAlignment attribute) (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) run() (in module MACS3.Commands.bdgbroadcall_cmd) (in module MACS3.Commands.bdgdiff_cmd) (in module MACS3.Commands.bdgpeakcall_cmd)

S

sample_num() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_num_copy() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_percent() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_percent_copy() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_percentage (MACS3.Signal.HMMR_EM.HMMR_EM attribute) save_bedGraph (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) save_SPMR (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) savitzky_golay() (in module MACS3.Signal.SignalProcessing) savitzky_golay_order2_deriv1() (in module MACS3.Signal.SignalProcessing) SB_score_ATAC() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) SB_score_ChIP() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) scan_window (MACS3.Signal.PeakModel.PeakModel attribute) score (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) ScoreTrackII (class in MACS3.Signal.ScoreTrack) scoring_method (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) se_all_in_one_pileup() (in module MACS3.Signal.Pileup) seed (MACS3.Signal.HMMR_EM.HMMR_EM attribute) SEQ (MACS3.Signal.ReadAlignment.ReadAlignment attribute) seq (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) set_pseudocount() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) set_rlengths() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method)

set_single_value() (MACS3.Signal.BedGraph.bedGraphTrackI method) shifted_line (MACS3.Signal.PeakModel.PeakModel attribute) size (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) smooth() (in module MACS3.Signal.PeakModel) sort() (MACS3.IO.PeakIO.PeakIO method) (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.Region.Regions method) (MACS3.Signal.UnitigRACollection.UnitigCollection method) sorted (MACS3.Signal.RACollection.RACollection attribute) sqrt() (in module MACS3.Signal.BedGraph) (in module MACS3.Signal.CallPeakUnit) (in module MACS3.Signal.SignalProcessing) start (MACS3.IO.PeakIO.BroadPeakContent attribute) (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.Signal.PeakVariants.PeakVariants attribute) strand (MACS3.Signal.ReadAlignment.ReadAlignment attribute) StrandFormatError subpeak_letters() (in module MACS3.IO.PeakIO) (in module MACS3.Signal.PeakDetect) subset() (MACS3.Signal.PairedEndTrack.PETrackII method) subtract_func() (in module MACS3.Signal.BedGraph) summary (MACS3.Signal.PeakModel.PeakModel attribute) summary() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) summit (MACS3.IO.PeakIO.PeakContent attribute)

T

t1bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) t2bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute) tag_expansion_size (MACS3.Signal.PeakModel.PeakModel attribute) thickEnd (MACS3.IO.PeakIO.BroadPeakContent attribute) thickStart (MACS3.IO.PeakIO.BroadPeakContent attribute) to_summits_bed() (MACS3.IO.PeakIO.PeakIO method) to_vcf() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) tobed() (MACS3.IO.PeakIO.PeakIO method) too_flat() (in module MACS3.Signal.SignalProcessing) top12alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) top12alleles_ratio (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) top1allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) top1isreference() (MACS3.Signal.PeakVariants.Variant method) top2allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute) top2isreference() (MACS3.Signal.PeakVariants.Variant method) total (MACS3.IO.PeakIO.PeakIO attribute) (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) (MACS3.Signal.Region.Regions attribute)

total() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) total_length() (MACS3.Signal.Region.Regions method) toVariant() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) toVCF() (MACS3.Signal.PeakVariants.PeakVariants method) (MACS3.Signal.PeakVariants.Variant method) trackline (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) treat (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) treat_edm (MACS3.Signal.ScoreTrack.ScoreTrackII attribute) treat_scaling_factor (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) treatment (MACS3.Signal.PeakModel.PeakModel attribute) TwoConditionScores (class in MACS3.Signal.ScoreTrack) type (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)

U

uint32_t() (in module MACS3.Signal.Prob) uint64_t() (in module MACS3.Signal.Prob) umfold (MACS3.Signal.PeakModel.PeakModel attribute) unitig_aln (MACS3.Signal.UnitigRACollection.UnitigRAs attribute) unitig_length (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)

UnitigCollection (class in MACS3.Signal.UnitigRACollection) UnitigRAs (class in MACS3.Signal.UnitigRACollection) update_top_alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) URAs_left (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) URAs_list (MACS3.Signal.UnitigRACollection.UnitigCollection attribute) URAs_right (MACS3.Signal.UnitigRACollection.UnitigCollection attribute)

V

v_alt_allele (MACS3.Signal.PeakVariants.Variant attribute) v_AR (MACS3.Signal.PeakVariants.Variant attribute) v_BIC_heter_AS (MACS3.Signal.PeakVariants.Variant attribute) v_BIC_heter_noAS (MACS3.Signal.PeakVariants.Variant attribute) v_BIC_homo_major (MACS3.Signal.PeakVariants.Variant attribute) v_BIC_homo_minor (MACS3.Signal.PeakVariants.Variant attribute) v_deltaBIC (MACS3.Signal.PeakVariants.Variant attribute) v_DP (MACS3.Signal.PeakVariants.Variant attribute) v_DP1C (MACS3.Signal.PeakVariants.Variant attribute) v_DP1T (MACS3.Signal.PeakVariants.Variant attribute) v_DP2C (MACS3.Signal.PeakVariants.Variant attribute) v_DP2T (MACS3.Signal.PeakVariants.Variant attribute) v_DPC (MACS3.Signal.PeakVariants.Variant attribute) v_DPT (MACS3.Signal.PeakVariants.Variant attribute) v_filter (MACS3.Signal.PeakVariants.Variant attribute) v_GQ (MACS3.Signal.PeakVariants.Variant attribute)

v_GT (MACS3.Signal.PeakVariants.Variant attribute) v_MINUS1T (MACS3.Signal.PeakVariants.Variant attribute) v_MINUS2T (MACS3.Signal.PeakVariants.Variant attribute) v_mutation_type (MACS3.Signal.PeakVariants.Variant attribute) v_PL_00 (MACS3.Signal.PeakVariants.Variant attribute) v_PL_01 (MACS3.Signal.PeakVariants.Variant attribute) v_PL_11 (MACS3.Signal.PeakVariants.Variant attribute) v_PLUS1T (MACS3.Signal.PeakVariants.Variant attribute) v_PLUS2T (MACS3.Signal.PeakVariants.Variant attribute) v_ref_allele (MACS3.Signal.PeakVariants.Variant attribute) v_ref_pos (MACS3.Signal.PeakVariants.Variant attribute) v_top1allele (MACS3.Signal.PeakVariants.Variant attribute) v_top2allele (MACS3.Signal.PeakVariants.Variant attribute) v_type (MACS3.Signal.PeakVariants.Variant attribute) Variant (class in MACS3.Signal.PeakVariants) verify_alns() (MACS3.Signal.RACollection.RACollection method)

W

warn (MACS3.Signal.PeakModel.PeakModel attribute) write_bedGraph() (MACS3.IO.BedGraphIO.bedGraphIO method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) write_matrix() (MACS3.Signal.ScoreTrack.TwoConditionScores method) write_to_bed() (MACS3.IO.PeakIO.PeakIO method) (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.Region.Regions method)

write_to_Bed12() (MACS3.IO.PeakIO.BroadPeakIO method) write_to_broadPeak() (MACS3.IO.PeakIO.BroadPeakIO method) write_to_gappedPeak() (MACS3.IO.PeakIO.BroadPeakIO method) write_to_narrowPeak() (MACS3.IO.PeakIO.PeakIO method) write_to_summit_bed() (MACS3.IO.PeakIO.PeakIO method) write_to_xls() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method)

X

xcorr (MACS3.Signal.PeakModel.PeakModel attribute)

Y

ycorr (MACS3.Signal.PeakModel.PeakModel attribute)

Z

zbdg_write() (in module MACS3.IO.OutputWriter)

zwig_write() (in module MACS3.IO.OutputWriter)