bio.vcf
¶
Source code: bio/vcf.seq
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bio.vcf.
BCF_UN_STR
¶
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bio.vcf.
BCF_UN_FLT
¶
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bio.vcf.
BCF_UN_INFO
¶
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bio.vcf.
BCF_UN_SHR
¶
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bio.vcf.
BCF_UN_FMT
¶
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bio.vcf.
BCF_UN_IND
¶
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bio.vcf.
BCF_UN_ALL
¶
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bio.vcf.
BCF_HL_FLT
¶
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bio.vcf.
BCF_HL_INFO
¶
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bio.vcf.
BCF_HL_FMT
¶
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bio.vcf.
BCF_HL_CTG
¶
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bio.vcf.
BCF_HL_STR
¶
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bio.vcf.
BCF_HL_GEN
¶
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bio.vcf.
BCF_HT_FLAG
¶
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bio.vcf.
BCF_HT_INT
¶
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bio.vcf.
BCF_HT_REAL
¶
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bio.vcf.
BCF_HT_STR
¶
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bio.vcf.
BCF_VL_FIXED
¶
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bio.vcf.
BCF_VL_VAR
¶
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bio.vcf.
BCF_VL_A
¶
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bio.vcf.
BCF_VL_G
¶
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bio.vcf.
BCF_VL_R
¶
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bio.vcf.
BCF_DT_ID
¶
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bio.vcf.
BCF_DT_CTG
¶
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bio.vcf.
BCF_DT_SAMPLE
¶
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bio.vcf.
BCF_BT_NULL
¶
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bio.vcf.
BCF_BT_INT8
¶
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bio.vcf.
BCF_BT_INT16
¶
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bio.vcf.
BCF_BT_INT32
¶
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bio.vcf.
BCF_BT_FLOAT
¶
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bio.vcf.
BCF_BT_CHAR
¶
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bio.vcf.
BCF_AUX_NONE
¶
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bio.vcf.
INT8_MIN
¶
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bio.vcf.
INT16_MIN
¶
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bio.vcf.
INT32_MIN
¶
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bio.vcf.
bcf_int8_vector_end
¶
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bio.vcf.
bcf_int16_vector_end
¶
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bio.vcf.
bcf_int32_vector_end
¶
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bio.vcf.
bcf_str_vector_end
¶
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bio.vcf.
bcf_int8_missing
¶
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bio.vcf.
bcf_int16_missing
¶
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bio.vcf.
bcf_int32_missing
¶
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bio.vcf.
bcf_float_missing
¶
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bio.vcf.
bcf_float_vector_end
¶
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bio.vcf.
bcf_str_missing
¶
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bio.vcf.
ptr_off
[T]
(base: ptr[byte], byte_offset: int)¶
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bio.vcf.
check_header_id
(hdr: ptr[_bcf_hdr_t], h1_type: i32, id: i32)¶
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bio.vcf.
is_gt_fmt
(hdr: ptr[_bcf_hdr_t], fmt_id: i32)¶
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bio.vcf.
bcf_float_is_missing
(f: i32)¶
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bio.vcf.
bcf_float_is_vector_end
(f: i32)¶
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bio.vcf.
bcf_gt_allele
(val: int)¶
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type
bio.vcf.
BCFHeaderMetaData
¶ Properties:
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type_code
¶
Magic methods:
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__init__
(bcf_hdr: ptr[_bcf_hdr_t], _type_code: int)
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__len__
()
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__iter__
()
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type
bio.vcf.
BCFHeaderContigs
¶ Magic methods:
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__init__
(bcf_hdr: ptr[_bcf_hdr_t])
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__iter__
()
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type
bio.vcf.
BCFHeaderSamples
¶ Magic methods:
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__init__
(bcf_hdr: ptr[_bcf_hdr_t])
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__iter__
()
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__getitem__
(index: int)
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bio.vcf.
METADATA_TYPES
¶
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type
bio.vcf.
BCFHeaderRecord
¶ Properties:
Magic methods:
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__init__
(bcf_hdr: ptr[_bcf_hdr_t], bcf_hrec: ptr[_bcf_hrec_t])
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__getitem__
(key: str)
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__iter__
()
Methods:
-
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type
bio.vcf.
BCFHeader
¶ Properties:
Magic methods:
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__init__
(bcf_hdr: ptr[_bcf_hdr_t])
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__init__
()
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__iter__
()
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bio.vcf.
VALUE_TYPES
¶
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type
bio.vcf.
BCFMetadata
¶ Properties:
Magic methods:
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__init__
(bcf_hdr: ptr[_bcf_hdr_t], _type_code: int, _id: int)
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type
bio.vcf.
BCFAux
¶ Properties:
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bio.vcf.
bcf_get_value_count
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t], h1_type: i32, id: i32, sample: i32)¶
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bio.vcf.
bcf_array_to_object
(data: cobj, type_code: i32, n: i32, count: i64, scalar: i32)¶
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bio.vcf.
bcf_info_get_value
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t], info: ptr[_bcf_info_t])¶
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bio.vcf.
try_unpack
(bcf1: ptr[_bcf1_t], mode: i32)¶
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type
bio.vcf.
VCFRecordInfo
¶ Magic methods:
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__init__
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
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__iter__
()
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__len__
()
Methods:
-
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type
bio.vcf.
VCFRecordSample
¶ Properties:
Magic methods:
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__init__
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t], index: int)
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__str__
()
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type
bio.vcf.
VCFRecordSamples
¶ Magic methods:
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__init__
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
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__len__
()
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__iter__
()
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__getitem__
(key: str)
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type
bio.vcf.
VCFRecordFormat
¶ Magic methods:
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__init__
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
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__len__
()
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__iter__
()
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__getitem__
(key: str)
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type
bio.vcf.
VCFRecordFilter
¶ Magic methods:
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__init__
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
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__iter__
()
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__getitem__
(key: str)
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__len__
()
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type
bio.vcf.
VCFRecord
¶ Properties:
Magic methods:
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__init__
(bcf1: ptr[_bcf1_t], bcf_hdr: ptr[_bcf_hdr_t])
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__str__
()
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class
bio.vcf.
BCFReader
¶ Properties:
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_bcf_hdr
¶
Magic methods:
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__init__
(path: str, unpack_all: bool, copy: bool)
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__iter__
()
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__enter__
()
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__exit__
()
Methods:
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close
()¶
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bio.vcf.
BCF
(path: str, unpack_all: bool = True, copy: bool = True)¶
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bio.vcf.
VCF
(path: str, unpack_all: bool = True, copy: bool = True)¶