bio.bwa

Source code: bio/bwa.seq

bio.bwa.BWA_LIB
type bio.bwa.bntann1_t
type bio.bwa.bntamb1_t
type bio.bwa.bntseq_t
type bio.bwa.mem_alnreg_t

Properties:

rb
re
qb
qe
rid
score
true_score
sub
alt_score
csub
sub_n
w
seedcov
secondary
secondary_all
type bio.bwa.mem_aln_t

Properties:

pos
rid
rev
alt
mapq
NM
cigar
score
sub
alt_score

Magic methods:

__init__()
type bio.bwa.mem_alnreg_v

Magic methods:

__init__()
__getitem__(idx: int)
__len__()
__iter__()
type bio.bwa.bwaidx_t

Methods:

name(aln: mem_aln_t)
bio.bwa.mem_opt_init()
bio.bwa.bwa_fill_scmat()
bio.bwa.bwa_idx_load()
bio.bwa.mem_align1()
bio.bwa.mem_reg2aln()
bio.bwa.options(match_score: int = 1, mismatch_score: int = 4, open_del: int = 6, open_ins: int = 6, extend_del: int = 1, extend_ins: int = 1, bandwidth: int = 100, zdrop: int = 100, clip_penalty: tuple[int, int] = (5, 5), unpaired_penalty: int = 17)
type bio.bwa.BWA

Magic methods:

__init__(hint: str)
__init__(opt: cobj, hint: str)

Methods:

name(aln: mem_aln_t)
reg2aln(s: seq, reg: mem_alnreg_t)
align(s: seq)