MACS3.Signal.PosReadsInfo module
All Parser classes
- class MACS3.Signal.PosReadsInfo.PosReadsInfo(ref_pos, ref_allele)
Bases:
object-
BIC_heter_AS:
typedef
-
BIC_heter_noAS:
typedef
-
BIC_homo_major:
typedef
-
BIC_homo_minor:
typedef
-
GQ:
typedef
-
GQ_heter_AS:
typedef
-
GQ_heter_ASsig:
typedef
-
GQ_heter_noAS:
typedef
-
GQ_homo_major:
typedef
-
GT:
str
-
PL_00:
typedef
-
PL_01:
typedef
-
PL_11:
typedef
- 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:
typedef
-
fermiNTs:
bytearray
- filterflag()
- Return type:
_fake_callable
-
filterout:
_fake_callable
-
hasfermiinfor:
_fake_callable
-
heter_AS_alleleratio:
typedef
-
heter_AS_kc:
typedef
-
heter_AS_ki:
typedef
-
heter_noAS_kc:
typedef
-
heter_noAS_ki:
typedef
-
lnL_heter_AS:
typedef
-
lnL_heter_noAS:
typedef
-
lnL_homo_major:
typedef
-
lnL_homo_minor:
typedef
-
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:
typedef
- toVariant()
- to_vcf()
Output REF,ALT,QUAL,FILTER,INFO,FORMAT, SAMPLE columns.
- Return type:
str
- top12alleles()
-
top12alleles_ratio:
typedef
-
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
-
BIC_heter_AS:
- MACS3.Signal.PosReadsInfo.bool(*args, **kwargs)