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: long
- 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: long
- 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: float
- v_BIC_heter_AS: float
- v_BIC_heter_noAS: float
- v_BIC_homo_major: float
- v_BIC_homo_minor: float
- v_DP: int
- v_DP1C: int
- v_DP1T: int
- v_DP2C: int
- v_DP2T: int
- v_DPC: int
- v_DPT: int
- v_GQ: int
- v_GT: str
- v_MINUS1T: int
- v_MINUS2T: int
- v_PLUS1T: int
- v_PLUS2T: int
- v_PL_00: int
- v_PL_01: int
- v_PL_11: int
- v_alt_allele: str
- v_deltaBIC: float
- v_filter: str
- v_mutation_type: str
- v_ref_allele: str
- v_ref_pos: long
- v_top1allele: str
- v_top2allele: str
- v_type: str
- MACS3.Signal.PeakVariants.bool(*args, **kwargs)