MACS3.Signal.PeakVariants module

Module for SAPPER PeakVariants class.

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file COPYING included with the distribution).

class MACS3.Signal.PeakVariants.PeakVariants(chrom, start, end, s)

Bases: object

add_variant(p, v)

chrom: str

d_Variants: dict

end: typedef

fix_indels()

get_refer_biased_01s()

Return type:: list

has_indel()

Return type:: _fake_callable

has_refer_biased_01()

Return type:: _fake_callable

n_variants()

Return type:: typedef

refseq: bytes

remove_variant(p)

replace_variant(p, v)

start: typedef

toVCF()

Return type:: str

class MACS3.Signal.PeakVariants.Variant(ref_allele, alt_allele, GQ, filter, type, mutation_type, top1allele, top2allele, DPT, DPC, DP1T, DP2T, DP1C, DP2C, PLUS1T, PLUS2T, MINUS1T, MINUS2T, deltaBIC, BIC_homo_major, BIC_homo_minor, BIC_heter_noAS, BIC_heter_AS, AR, GT, DP, PL_00, PL_01, PL_11)

Bases: object

is_indel()

Return type:: _fake_callable

is_only_del()

Return type:: _fake_callable

is_only_insertion()

Return type:: _fake_callable

is_refer_biased_01(ar=0.85)

Return type:: _fake_callable

toVCF()

Return type:: str

top1isreference()

Return type:: _fake_callable

top2isreference()

Return type:: _fake_callable

v_AR: typedef

v_BIC_heter_AS: typedef

v_BIC_heter_noAS: typedef

v_BIC_homo_major: typedef

v_BIC_homo_minor: typedef

v_DP: typedef

v_DP1C: typedef

v_DP1T: typedef

v_DP2C: typedef

v_DP2T: typedef

v_DPC: typedef

v_DPT: typedef

v_GQ: typedef

v_GT: str

v_MINUS1T: typedef

v_MINUS2T: typedef

v_PLUS1T: typedef

v_PLUS2T: typedef

v_PL_00: typedef

v_PL_01: typedef

v_PL_11: typedef

v_alt_allele: str

v_deltaBIC: typedef

v_filter: str

v_mutation_type: str

v_ref_allele: str

v_ref_pos: typedef

v_top1allele: str

v_top2allele: str

v_type: str

MACS3.Signal.PeakVariants.bool(*args, **kwargs)