bio.vcf

Source code: bio/vcf.seq

bio.vcf.BCF_UN_STR
bio.vcf.BCF_UN_FLT
bio.vcf.BCF_UN_INFO
bio.vcf.BCF_UN_SHR
bio.vcf.BCF_UN_FMT
bio.vcf.BCF_UN_IND
bio.vcf.BCF_UN_ALL
bio.vcf.BCF_HL_FLT
bio.vcf.BCF_HL_INFO
bio.vcf.BCF_HL_FMT
bio.vcf.BCF_HL_CTG
bio.vcf.BCF_HL_STR
bio.vcf.BCF_HL_GEN
bio.vcf.BCF_HT_FLAG
bio.vcf.BCF_HT_INT
bio.vcf.BCF_HT_REAL
bio.vcf.BCF_HT_STR
bio.vcf.BCF_VL_FIXED
bio.vcf.BCF_VL_VAR
bio.vcf.BCF_VL_A
bio.vcf.BCF_VL_G
bio.vcf.BCF_VL_R
bio.vcf.BCF_DT_ID
bio.vcf.BCF_DT_CTG
bio.vcf.BCF_DT_SAMPLE
bio.vcf.BCF_BT_NULL
bio.vcf.BCF_BT_INT8
bio.vcf.BCF_BT_INT16
bio.vcf.BCF_BT_INT32
bio.vcf.BCF_BT_FLOAT
bio.vcf.BCF_BT_CHAR
bio.vcf.BCF_AUX_NONE
bio.vcf.INT8_MIN
bio.vcf.INT16_MIN
bio.vcf.INT32_MIN
bio.vcf.bcf_int8_vector_end
bio.vcf.bcf_int16_vector_end
bio.vcf.bcf_int32_vector_end
bio.vcf.bcf_str_vector_end
bio.vcf.bcf_int8_missing
bio.vcf.bcf_int16_missing
bio.vcf.bcf_int32_missing
bio.vcf.bcf_float_missing
bio.vcf.bcf_float_vector_end
bio.vcf.bcf_str_missing
bio.vcf.ptr_off[T](base: ptr[byte], byte_offset: int)
bio.vcf.check_header_id(hdr: ptr[_bcf_hdr_t], h1_type: i32, id: i32)
bio.vcf.is_gt_fmt(hdr: ptr[_bcf_hdr_t], fmt_id: i32)
bio.vcf.bcf_float_is_missing(f: i32)
bio.vcf.bcf_float_is_vector_end(f: i32)
bio.vcf.bcf_gt_allele(val: int)
type bio.vcf.BCFHeaderMetaData

Properties:

type_code

Magic methods:

__init__(bcf_hdr: ptr[_bcf_hdr_t], _type_code: int)
__len__()
__iter__()
type bio.vcf.BCFHeaderContigs

Magic methods:

__init__(bcf_hdr: ptr[_bcf_hdr_t])
__iter__()
type bio.vcf.BCFHeaderSamples

Magic methods:

__init__(bcf_hdr: ptr[_bcf_hdr_t])
__iter__()
__getitem__(index: int)
bio.vcf.METADATA_TYPES
type bio.vcf.BCFHeaderRecord

Properties:

hdr_type
key
value
attrs

Magic methods:

__init__(bcf_hdr: ptr[_bcf_hdr_t], bcf_hrec: ptr[_bcf_hrec_t])
__getitem__(key: str)
__iter__()

Methods:

get(key: str)
iterkeys()
itervalues()
iteritems()
type bio.vcf.BCFHeader

Properties:

info
filters
formats
contigs
samples

Magic methods:

__init__(bcf_hdr: ptr[_bcf_hdr_t])
__init__()
__iter__()
bio.vcf.VALUE_TYPES
type bio.vcf.BCFMetadata

Properties:

name
bcf_type
record
description

Magic methods:

__init__(bcf_hdr: ptr[_bcf_hdr_t], _type_code: int, _id: int)
type bio.vcf.BCFAux

Properties:

val
arr
type_code
is_array
bio.vcf.bcf_get_value_count(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t], h1_type: i32, id: i32, sample: i32)
bio.vcf.bcf_array_to_object(data: cobj, type_code: i32, n: i32, count: i64, scalar: i32)
bio.vcf.bcf_info_get_value(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t], info: ptr[_bcf_info_t])
bio.vcf.try_unpack(bcf1: ptr[_bcf1_t], mode: i32)
type bio.vcf.VCFRecordInfo

Magic methods:

__init__(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
__iter__()
__len__()

Methods:

get_int(key: str)
get_ints(key: str)
get_float(key: str)
get_floats(key: str)
get_str(key: str)
get_flag(key: str)
type bio.vcf.VCFRecordSample

Properties:

name
alleles

Magic methods:

__init__(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t], index: int)
__str__()
type bio.vcf.VCFRecordSamples

Magic methods:

__init__(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
__len__()
__iter__()
__getitem__(key: str)
type bio.vcf.VCFRecordFormat

Magic methods:

__init__(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
__len__()
__iter__()
__getitem__(key: str)
type bio.vcf.VCFRecordFilter

Magic methods:

__init__(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
__iter__()
__getitem__(key: str)
__len__()
type bio.vcf.VCFRecord

Properties:

info
n_info
chrom
contig
pos
qual
ref
alts
id
rlen

Magic methods:

__init__(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
__str__()
class bio.vcf.BCFReader

Properties:

_bcf_hdr

Magic methods:

__init__(path: str, unpack_all: bool, copy: bool)
__iter__()
__enter__()
__exit__()

Methods:

close()
bio.vcf.BCF(path: str, unpack_all: bool = True, copy: bool = True)
bio.vcf.VCF(path: str, unpack_all: bool = True, copy: bool = True)