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|
import sys
from typing import (
Optional,
Union,
Any,
Sequence,
Tuple,
Iterator,
List,
Iterable,
Dict,
overload,
TypeVar,
Mapping,
Generic,
)
if sys.version_info < (3, 8):
from typing_extensions import Literal
else:
from typing import Literal
from pysam.libchtslib import HTSFile, _HasFileNo
_D = TypeVar("_D")
_K = TypeVar("_K", str, Union[int, str])
_V = TypeVar("_V")
class _Mapping(Generic[_K, _V]):
def __len__(self) -> int: ...
def __contains__(self, key: _K) -> bool: ...
def __iter__(self) -> Iterator[_K]: ...
def iterkeys(self) -> Iterator[_K]: ...
def itervalues(self) -> Iterator[_V]: ...
def iteritems(self) -> Iterator[Tuple[_K, _V]]: ...
def keys(self) -> List[_K]: ...
def items(self) -> List[Tuple[_K, _V]]: ...
def values(self) -> List[_V]: ...
def __bool__(self) -> bool: ...
def __getitem__(self, key: _K) -> _V: ...
def get(self, key: _K, default: _D = ...) -> Union[_D, _V]: ...
class VariantHeaderRecord(_Mapping[str, str]):
@property
def header(self) -> VariantHeader: ...
@property
def type(self) -> Optional[str]: ...
@property
def key(self) -> Optional[str]: ...
@property
def value(self) -> Optional[str]: ...
@property
def attrs(self) -> Sequence[Tuple[str, str]]: ...
def update(self, items: Union[Iterable, Dict] = ..., **kwargs) -> None: ...
def pop(self, key: str, default: str = ...) -> str: ...
def remove(self) -> None: ... # crashes
class VariantHeaderRecords:
@property
def header(self) -> VariantHeader: ...
def __len__(self) -> int: ...
def __bool__(self) -> bool: ...
def __getitem__(self, index) -> VariantHeaderRecord: ...
def __iter__(self) -> Iterator[VariantHeaderRecord]: ...
class VariantMetadata:
@property
def header(self) -> VariantHeader: ...
@property
def name(self) -> str: ...
# @property # should this be exposed?
# def id(self) -> int: ...
@property
def number(self) -> Optional[str]: ...
@property
def type(self) -> Optional[str]: ...
@property
def description(self) -> Optional[str]: ...
@property
def record(self) -> Optional[VariantHeaderRecord]: ...
def remove_header(self) -> None: ...
class VariantHeaderMetadata(_Mapping[str, VariantMetadata]):
@property
def header(self) -> VariantHeader: ...
def add(
self,
id: str,
number: Optional[Union[int, str]],
type: Optional[str],
description: str,
**kwargs
) -> None: ...
def remove_header(self, key: str) -> None: ...
def clear_header(self) -> None: ...
class VariantContig:
@property
def header(self) -> VariantHeader: ...
@property
def name(self) -> str: ...
@property
def id(self) -> int: ...
@property
def length(self) -> Optional[int]: ...
@property
def header_record(self) -> VariantHeaderRecord: ...
def remove_header(self) -> None: ...
class VariantHeaderContigs(_Mapping[Union[int, str], VariantContig]):
@property
def header(self) -> VariantHeader: ...
def remove_header(self, key: Union[int, str]) -> None: ...
def clear_header(self) -> None: ...
def add(self, id: str, length: Optional[int] = ..., **kwargs) -> None: ...
class VariantHeaderSamples:
@property
def header(self) -> VariantHeader: ...
def __len__(self) -> int: ...
def __bool__(self) -> bool: ...
def __getitem__(self, index: int) -> str: ...
def __iter__(self) -> Iterator[str]: ...
def __contains__(self, key: str) -> bool: ...
def add(self, name: str) -> None: ...
class VariantHeader:
def __init__(self) -> None: ...
def __bool__(self) -> bool: ...
def copy(self) -> VariantHeader: ...
def merge(self, header: VariantHeader) -> None: ...
@property
def version(self) -> str: ...
@property
def samples(self) -> VariantHeaderSamples: ...
@property
def records(self) -> VariantHeaderRecords: ...
@property
def contigs(self) -> VariantHeaderContigs: ...
@property
def filters(self) -> VariantHeaderMetadata: ...
@property
def info(self) -> VariantHeaderMetadata: ...
@property
def formats(self) -> VariantHeaderMetadata: ...
@property
def alts(self) -> Dict[str, VariantHeaderRecord]: ...
def new_record(
self,
contig: Optional[str] = ...,
start: int = ...,
stop: int = ...,
alleles: Optional[Tuple[str, ...]] = ...,
id: Optional[str] = ...,
qual: Optional[float] = ...,
filter: Optional[Any] = ...,
info: Optional[Mapping[str, _InfoValue]] = ...,
samples: Optional[Iterable[Optional[Mapping[str, _FormatValue]]]] = ...,
**kwargs
) -> VariantRecord: ...
def add_record(self, record: VariantHeaderRecord) -> None: ...
def add_line(self, line: str) -> None: ...
@overload
def add_meta(
self, key: str, value: None = ..., items: Iterable[Tuple[str, str]] = ...
) -> None: ...
@overload
def add_meta(self, key: str, value: str = ..., items: None = ...) -> None: ...
def add_sample(self, name: str) -> None: ...
def add_samples(self, *args: Union[str, Iterable[str]]) -> None: ...
class VariantRecordFilter(_Mapping[Union[int, str], VariantMetadata]):
def add(self, key: str) -> None: ...
def __delitem__(self, key: Union[int, str]) -> None: ...
def clear(self) -> None: ...
def __eq__(self, other) -> bool: ...
def __ne__(self, other) -> bool: ...
class VariantRecordFormat(_Mapping[str, VariantMetadata]):
def __delitem__(self, key: str) -> None: ...
def clear(self) -> None: ...
_InfoValue = Any # TODO see bcf_info_get_value
class VariantRecordInfo(_Mapping[str, _InfoValue]):
def __setitem__(self, key: str, object: _InfoValue) -> None: ...
def __delitem__(self, key: str) -> None: ...
def clear(self) -> None: ...
def update(
self, items: Optional[_Mapping[str, _InfoValue]] = ..., **kwargs
) -> None: ...
def pop(self, key: str, default: _D = ...) -> Union[_D, _InfoValue]: ...
def __eq__(self, other) -> bool: ...
def __ne__(self, other) -> bool: ...
class VariantRecordSamples(_Mapping[Union[str, int], "VariantRecordSample"]):
def __eq__(self, other) -> bool: ...
def __ne__(self, other) -> bool: ...
# TODO Do these work? Isn’t the container read only?
def update(
self,
items: Optional[Mapping[Union[str, int], VariantRecordSample]] = ...,
**kwargs
) -> None: ...
def pop(
self, key: Union[str, int], default: _D = ...
) -> Union[_D, VariantRecordSample]: ...
class VariantRecord:
@property
def header(self) -> VariantHeader: ...
def copy(self) -> VariantRecord: ...
def translate(self, dst_header: VariantHeader) -> None: ...
rid: int
chrom: str
contig: str
pos: int
start: int
stop: int
rlen: int
qual: Optional[float]
id: Optional[str]
ref: Optional[str]
alleles: Optional[Tuple[str, ...]]
alts: Optional[Tuple[str, ...]]
@property
def filter(self) -> VariantRecordFilter: ...
@property
def info(self) -> VariantRecordInfo: ...
@property
def format(self) -> VariantRecordFormat: ...
@property
def samples(self) -> VariantRecordSamples: ...
def __eq__(self, other) -> bool: ...
def __ne__(self, other) -> bool: ...
_FormatValue = Any # TODO see bcf_format_get_value
class VariantRecordSample(_Mapping[str, _FormatValue]):
@property
def index(self) -> int: ...
@property
def name(self) -> str: ...
allele_indices: Optional[Tuple[Optional[int], ...]]
alleles: Optional[Tuple[Optional[str], ...]]
phased: bool
def __setitem__(self, key: str, value: _FormatValue) -> None: ...
def __delitem__(self, key: str) -> None: ...
def clear(self) -> None: ...
def update(
self, items: Optional[Mapping[str, _FormatValue]] = ..., **kwargs
) -> None: ...
def pop(self, key: str, default: _D = ...) -> Union[_D, _FormatValue]: ...
def __eq__(self, other) -> Any: ...
def __ne__(self, other) -> Any: ...
class BaseIndex(_Mapping[Union[int, str], str]):
refs: Sequence[str]
refmap: Dict[str, str]
def __init__(self) -> None: ...
# TODO Do these work? Isn’t the container read only?
def update(self, items: Optional[Mapping[str, str]] = ..., **kwargs) -> None: ...
def pop(self, key: str, default: _D = ...) -> Union[_D, str]: ...
class BCFIndex(BaseIndex):
@property
def header(self) -> VariantHeader: ...
def __init__(self) -> None: ...
def fetch(
self,
bcf: VariantFile,
contig: str,
start: Optional[int],
stop: Optional[int],
reopen: bool,
) -> BCFIterator: ...
class TabixIndex(BaseIndex):
def __init__(self) -> None: ...
def fetch(
self,
bcf: VariantFile,
contig: str,
start: Optional[int],
stop: Optional[int],
reopen: bool,
) -> TabixIterator: ...
class BaseIterator:
def __init__(self) -> None: ...
class BCFIterator(BaseIterator):
def __init__(
self,
bcf: VariantFile,
contig: str,
start: Optional[int] = ...,
stop: Optional[int] = ...,
reopen: bool = ...,
) -> None: ...
def __iter__(self) -> BCFIterator: ...
def __next__(self) -> VariantRecord: ...
class TabixIterator(BaseIterator):
def __init__(
self,
bcf: VariantFile,
contig: str,
start: Optional[int] = ...,
stop: Optional[int] = ...,
reopen: bool = ...,
) -> None: ...
def __iter__(self) -> TabixIterator: ...
def __next__(self) -> VariantRecord: ...
class VariantFile(HTSFile):
@property
def header(self) -> VariantHeader: ...
@property
def index(self) -> BaseIndex: ...
@property
def drop_samples(self) -> bool: ...
@property
def is_reading(self) -> bool: ...
@property
def header_written(self) -> bool: ...
def __init__(
self,
filename: Union[str, bytes, int, _HasFileNo],
mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ...,
index_filename: Optional[str] = ...,
header: Optional[VariantHeader] = ...,
drop_samples: bool = ...,
duplicate_filehandle: bool = ...,
ignore_truncation: bool = ...,
threads: int = ...,
) -> None: ...
def close(self) -> None: ...
def __iter__(self) -> VariantFile: ...
def __next__(self) -> VariantRecord: ...
def copy(self) -> VariantFile: ...
def open(
self,
filename: Union[str, bytes, int, _HasFileNo],
mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ...,
index_filename: Optional[str] = ...,
header: Optional[VariantHeader] = ...,
drop_samples: bool = ...,
duplicate_filehandle: bool = ...,
ignore_truncation: bool = ...,
threads: int = ...,
) -> None: ...
def reset(self) -> None: ...
def is_valid_tid(self, tid: int) -> bool: ...
def get_tid(self, reference: str) -> int: ...
def get_reference_name(self, tid: int) -> str: ...
def fetch(
self,
contig: Optional[str] = ...,
start: Optional[int] = ...,
stop: Optional[int] = ...,
region: Optional[str] = ...,
reopen: bool = ...,
end: Optional[int] = ...,
reference: Optional[str] = ...,
) -> Iterator[VariantRecord]: ...
def new_record(self, *args, **kwargs) -> Any: ...
def write(self, record: VariantRecord) -> int: ...
def subset_samples(self, include_samples: Iterable[str]) -> None: ...
|
