MACS3.Signal.PosReadsInfo module
All Parser classes
- class MACS3.Signal.PosReadsInfo.PosReadsInfo(ref_pos, ref_allele)
Bases:
object- BIC_heter_AS: double
- BIC_heter_noAS: double
- BIC_homo_major: double
- BIC_homo_minor: double
- GQ: double
- GQ_heter_AS: int
- GQ_heter_ASsig: int
- GQ_heter_noAS: int
- GQ_homo_major: int
- GT: str
- PL_00: double
- PL_01: double
- PL_11: double
- SB_score_ATAC(a, b, c, d)
calculate score for filtering variants with strange strand biases.
ATAC-seq version
a: top1/major allele plus strand b: top2/minor allele plus strand c: top1/major allele minus strand d: top2/minor allele minus strand
Return a value: cython.float so that if this value >= 1, the variant will be filtered out.
- Return type:
typedef
- SB_score_ChIP(a, b, c, d)
calculate score for filtering variants with strange strand biases.
a: top1/major allele plus strand b: top2/minor allele plus strand c: top1/major allele minus strand d: top2/minor allele minus strand
Return a value: cython.float so that if this value >= 1, the variant will be filtered out.
- Return type:
typedef
- add_C(read_index, read_allele, read_bq, strand, Q=20)
- add_T(read_index, read_allele, read_bq, strand, tip, Q=20)
Strand 0: plus, 1: minus
Q is the quality cutoff. By default, only consider Q20 or read_bq > 20.
- alt_allele: bytes
- apply_GQ_cutoff(min_homo_GQ=50, min_heter_GQ=100)
- apply_deltaBIC_cutoff(min_delta_BIC=10)
- bq_set_C: dict
- bq_set_T: dict
- call_GT(max_allowed_ar=0.99)
Require update_top_alleles being called.
- deltaBIC: double
- fermiNTs: bytearray
- filterflag()
- Return type:
_fake_callable
- filterout: _fake_callable
- hasfermiinfor: _fake_callable
- heter_AS_alleleratio: double
- heter_AS_kc: int
- heter_AS_ki: int
- heter_noAS_kc: int
- heter_noAS_ki: int
- lnL_heter_AS: double
- lnL_heter_noAS: double
- lnL_homo_major: double
- lnL_homo_minor: double
- mutation_type: str
- n_reads: dict
- n_reads_C: dict
- n_reads_T: dict
- n_strand: list
- n_tips: dict
- raw_read_depth(opt='all')
- Return type:
typedef
- ref_allele: bytes
- ref_pos: long
- toVariant()
- to_vcf()
Output REF,ALT,QUAL,FILTER,INFO,FORMAT, SAMPLE columns.
- Return type:
str
- top12alleles()
- top12alleles_ratio: float
- top1allele: bytes
- top2allele: bytes
- type: str
- update_top_alleles(min_top12alleles_ratio=0.8, min_altallele_count=2, max_allowed_ar=0.95)
Identify top1 and top2 NT. the ratio of (top1+top2)/total
- MACS3.Signal.PosReadsInfo.bool(*args, **kwargs)