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jpayne@68
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1 import sys
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2 from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar
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3
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4 if sys.version_info < (3, 8):
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5 from typing_extensions import Protocol
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6 else:
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7 from typing import Protocol
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8
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9 class _HasFileNo(Protocol):
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10 def fileno(self) -> int: ...
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11
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12 def get_verbosity() -> int: ...
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13 def set_verbosity(level: int): ...
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14
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15 THFile = TypeVar("THFile", bound="HFile")
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16
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17 class HFile:
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18 def __init__(self, name: Union[int, str], mode: str = ...) -> None: ...
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19 def __enter__(self: THFile) -> THFile: ...
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20 def __exit__(self, type, value, tb): ...
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21 def __iter__(self) -> Any: ...
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22 def __next__(self) -> str: ...
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23 @property
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24 def closed(self) -> bool: ...
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25 @property
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26 def mode(self) -> str: ...
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27 @property
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28 def name(self) -> Union[int, str]: ...
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29 def close(self) -> None: ...
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30 def fileno(self) -> int: ...
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31 def flush(self) -> None: ...
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32 def isatty(self) -> bool: ...
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33 def readable(self) -> bool: ...
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34 def read(self, size: int = ...) -> bytes: ...
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35 def readall(self) -> bytes: ...
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36 def readinto(self, buf: Any) -> bytes: ...
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37 def readline(self, size: int = ...) -> bytes: ...
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38 def readlines(self) -> List[bytes]: ...
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39 def seek(self, offset: int, whence: int = ...) -> int: ...
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40 def seekable(self) -> bool: ...
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41 def tell(self) -> int: ...
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42 def truncate(self, *args) -> NoReturn: ...
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43 def writable(self) -> bool: ...
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44 def write(self, b: bytes) -> int: ...
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45 def writelines(self, lines: Iterable[bytes]) -> None: ...
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46
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47 THTSFile = TypeVar("THTSFile", bound="HTSFile")
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48
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49 class HTSFile:
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50 def __enter__(self: THTSFile) -> THTSFile: ...
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51 def __exit__(self, type, value, traceback) -> Any: ...
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52 @property
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53 def filename(self) -> Any: ...
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54 @property
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55 def mode(self) -> str: ...
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56 @property
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57 def threads(self) -> int: ...
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58 @property
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59 def index_filename(self) -> Optional[str]: ...
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60 @property
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61 def is_stream(self) -> bool: ...
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62 @property
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63 def is_remote(self) -> bool: ...
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64 @property
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65 def duplicate_filehandle(self) -> bool: ...
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66 def close(self) -> None: ...
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67 def flush(self) -> None: ...
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68 def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
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69 @property
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70 def category(self) -> str: ...
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71 @property
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72 def format(self) -> str: ...
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73 @property
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74 def version(self) -> Tuple[int, int]: ...
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75 @property
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76 def compression(self) -> str: ...
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77 @property
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78 def description(self) -> str: ...
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79 @property
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80 def is_open(self) -> bool: ...
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81 @property
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82 def is_closed(self) -> bool: ...
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83 @property
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84 def closed(self) -> bool: ...
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85 @property
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86 def is_write(self) -> bool: ...
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87 @property
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88 def is_read(self) -> bool: ...
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89 @property
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90 def is_sam(self) -> bool: ...
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91 @property
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92 def is_bam(self) -> bool: ...
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93 @property
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94 def is_cram(self) -> bool: ...
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95 @property
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96 def is_vcf(self) -> bool: ...
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97 @property
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98 def is_bcf(self) -> bool: ...
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99 def reset(self) -> None: ...
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100 def seek(self, offset: int, whence: int = ...) -> int: ...
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101 def tell(self) -> int: ...
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102 def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ...
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103 def parse_region(
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104 self,
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105 contig: Optional[str] = ...,
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106 start: Optional[int] = ...,
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107 stop: Optional[int] = ...,
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108 region: Optional[str] = ...,
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109 tid: Optional[int] = ...,
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110 reference: Optional[str] = ...,
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111 end: Optional[int] = ...,
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112 ) -> Tuple[int, int, int, int]: ...
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113 def is_valid_tid(self, tid: int) -> bool: ...
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114 def is_valid_reference_name(self, contig: str) -> bool: ...
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115 def get_tid(self, contig: str) -> int: ...
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116 def get_reference_name(self, tid: int) -> Optional[str]: ...
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