Index

_

__flag_sorted (MACS3.IO.PeakIO.RegionIO attribute)

A

add() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.ScoreTrack.ScoreTrackII 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) add_loc() (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack 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_variant() (MACS3.Signal.PeakVariants.PeakVariants method) alternative_d (MACS3.Signal.PeakModel.PeakModel attribute) annotation (MACS3.Signal.FixWidthTrack.FWTrack attribute) apply_deltaBIC_cutoff() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) apply_func() (MACS3.Signal.BedGraph.bedGraphTrackI method) apply_GQ_cutoff() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)

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) baseline_value (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII 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) binomial_cdf() (in module MACS3.Signal.Prob) binomial_cdf_inv() (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) BroadPeakContent (class in MACS3.IO.PeakIO) BroadPeakIO (class in MACS3.IO.PeakIO) buffer_size (MACS3.Signal.FixWidthTrack.FWTrack attribute) build() (MACS3.Signal.PeakModel.PeakModel method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) build_unitig_collection() (MACS3.Signal.RACollection.RACollection method)

C

calculate_GQ() (in module MACS3.Signal.VariantStat) calculate_GQ_heterASsig() (in module MACS3.Signal.VariantStat) call_broadpeaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII 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.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) 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) chisq_logp_e() (in module MACS3.Signal.Prob) chisq_pvalue_e() (in module MACS3.Signal.Prob) chrom (MACS3.IO.PeakIO.PeakContent attribute) close() (MACS3.IO.BAM.BAMaccessor method) CO_sorted (MACS3.IO.PeakIO.PeakIO attribute), [1] coffset_cache (MACS3.IO.BAM.BAMaccessor attribute) compute_region_tags_from_peaks() (MACS3.Signal.FixWidthTrack.FWTrack method) cutoff_analysis() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.ScoreTrack.ScoreTrackII method)

D

d (MACS3.Signal.PeakModel.PeakModel attribute) destroy() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method)

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

E

enable_trackline() (MACS3.Signal.ScoreTrack.ScoreTrackII method) end (MACS3.IO.PeakIO.PeakContent attribute) enforce_peakyness() (in module MACS3.Signal.SignalProcessing) enforce_valleys() (in module MACS3.Signal.SignalProcessing) exclude() (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.Region.Regions method)

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.PeakContent attribute) filename (MACS3.IO.BAM.BAIFile attribute) filter_dup() (MACS3.Signal.FixWidthTrack.FWTrack 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) filterflag() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) finalize() (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) fix_indels() (MACS3.Signal.PeakVariants.PeakVariants method) 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_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.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_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_locations_by_chr() (MACS3.Signal.FixWidthTrack.FWTrack method) get_memory_usage() (MACS3.Utilities.Logger.MemoryLogger static method) get_metadata_by_refseq() (MACS3.IO.BAM.BAIFile method) get_PosReadsInfo_ref_pos() (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.UnitigRACollection.UnitigCollection method) 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) get_variant_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) (MACS3.Signal.UnitigRACollection.UnitigRAs method)

H

has_indel() (MACS3.Signal.PeakVariants.PeakVariants method) has_refer_biased_01() (MACS3.Signal.PeakVariants.PeakVariants method) 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)

I

init_from_PeakIO() (MACS3.Signal.Region.Regions method) intersect() (MACS3.Signal.Region.Regions method) 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)

L

length (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.Signal.FixWidthTrack.FWTrack 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.FixWidthTrack module MACS3.Signal.HMMR_HMM module MACS3.Signal.HMMR_Signal_Processing 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_ScoreTrackII_for_macs() (MACS3.Signal.BedGraph.bedGraphTrackI method) mapping_function_always_1() (in module MACS3.Signal.PileupV2) maxima() (in module MACS3.Signal.SignalProcessing) maxvalue (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) MemoryLogger (class in MACS3.Utilities.Logger) merge_overlap() (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.Region.Regions method) metadata (MACS3.IO.BAM.BAIFile 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.FixWidthTrack MACS3.Signal.HMMR_HMM MACS3.Signal.HMMR_Signal_Processing 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

N

n_bins (MACS3.IO.BAM.BAIFile attribute) n_chunks (MACS3.IO.BAM.BAIFile attribute) n_edits_sum() (MACS3.Signal.RACollection.RACollection method) n_mapped (MACS3.IO.BAM.BAIFile attribute) n_ref (MACS3.IO.BAM.BAIFile 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.PeakContent attribute) (MACS3.IO.PeakIO.PeakIO attribute), [1] noffset_cache (MACS3.IO.BAM.BAMaccessor attribute) NotEnoughPairsException

O

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) PeakContent (class in MACS3.IO.PeakIO) PeakIO (class in MACS3.IO.PeakIO) PeakModel (class in MACS3.Signal.PeakModel) peaks (MACS3.IO.PeakIO.BroadPeakIO attribute), [1] (MACS3.IO.PeakIO.PeakIO attribute), [1] PeakVariants (class in MACS3.Signal.PeakVariants) pileup (MACS3.IO.PeakIO.PeakContent attribute) pileup_a_chromosome() (MACS3.Signal.FixWidthTrack.FWTrack method) pileup_a_chromosome_c() (MACS3.Signal.FixWidthTrack.FWTrack method) pileup_and_write_pe() (in module MACS3.Signal.Pileup) pileup_and_write_se() (in module MACS3.Signal.Pileup) 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) plus_line (MACS3.Signal.PeakModel.PeakModel attribute) pnorm() (in module MACS3.Signal.Prob) pnorm2() (in module MACS3.Signal.Prob) 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) print_to_bed() (MACS3.Signal.FixWidthTrack.FWTrack method) pscore (MACS3.IO.PeakIO.PeakContent attribute)

Q

qscore (MACS3.IO.PeakIO.PeakContent attribute)

quick_pileup() (in module MACS3.Signal.Pileup)

R

RACollection (class in MACS3.Signal.RACollection) randomly_pick() (MACS3.IO.PeakIO.PeakIO method) 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) references (MACS3.IO.BAM.BAMaccessor attribute) refine_peaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) RegionIO (class in MACS3.IO.PeakIO)

Regions (class in MACS3.Signal.Region) regions (MACS3.IO.PeakIO.RegionIO attribute) (MACS3.Signal.Region.Regions attribute), [1] 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) rlengths (MACS3.IO.BAM.BAMaccessor 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) sample_percent() (MACS3.Signal.FixWidthTrack.FWTrack method) savitzky_golay() (in module MACS3.Signal.SignalProcessing) savitzky_golay_order2_deriv1() (in module MACS3.Signal.SignalProcessing) scan_window (MACS3.Signal.PeakModel.PeakModel attribute) score (MACS3.IO.PeakIO.PeakContent attribute) ScoreTrackII (class in MACS3.Signal.ScoreTrack) se_all_in_one_pileup() (in module MACS3.Signal.Pileup) set_pseudocount() (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) set_rlengths() (MACS3.Signal.FixWidthTrack.FWTrack method) set_single_value() (MACS3.Signal.BedGraph.bedGraphTrackI method)

shifted_line (MACS3.Signal.PeakModel.PeakModel 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.RACollection.RACollection method) (MACS3.Signal.Region.Regions method) (MACS3.Signal.UnitigRACollection.UnitigCollection method) start (MACS3.IO.PeakIO.PeakContent attribute) summary() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) summit (MACS3.IO.PeakIO.PeakContent attribute)

T

to_summits_bed() (MACS3.IO.PeakIO.PeakIO method) to_vcf() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) tobed() (MACS3.IO.PeakIO.PeakIO method) top12alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) top1isreference() (MACS3.Signal.PeakVariants.Variant method) top2isreference() (MACS3.Signal.PeakVariants.Variant method) total (MACS3.IO.PeakIO.PeakIO attribute), [1] (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.Region.Regions attribute), [1]

total() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII 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) TwoConditionScores (class in MACS3.Signal.ScoreTrack)

U

UnitigCollection (class in MACS3.Signal.UnitigRACollection)

UnitigRAs (class in MACS3.Signal.UnitigRACollection) update_top_alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)

V

Variant (class in MACS3.Signal.PeakVariants)

W

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)