`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)¶

bio.vcf¶

`bio.vcf`¶