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1 import sys
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2 from typing import Optional, List, Any
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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 Literal
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6 else:
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7 from typing import Literal
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8
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9 from pysam.libchtslib import HTSFile
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10
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11 _ParseResult = Any
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12
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13 class Parser:
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14 def __init__(self, encoding: str = ...) -> None: ...
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15 def get_encoding(self) -> str: ...
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16 def set_encoding(self, encoding: str) -> None: ...
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17 def __call__(self, buffer: str, length: int) -> _ParseResult: ...
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18
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19 class asTuple(Parser): ...
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20 class asGFF3(Parser): ...
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21 class asGTF(Parser): ...
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22 class asBed(Parser): ...
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23 class asVCF(Parser): ...
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24
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25 class TabixFile(HTSFile):
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26 filename_index: bytes = ...
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27 @property
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28 def header(self) -> List[str]: ...
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29 @property
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30 def contigs(self) -> List[str]: ...
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31 def __init__(
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32 self,
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33 filename: str,
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34 mode: str = ...,
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35 parser: Parser = ...,
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36 index: Optional[str] = ...,
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37 encoding: str = ...,
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38 threads: int = ...,
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39 *args,
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40 **kwargs
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41 ) -> None: ...
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42 def fetch(
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43 self,
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44 reference: Optional[str] = ...,
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45 start: Optional[int] = ...,
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46 end: Optional[int] = ...,
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47 region: Optional[str] = ...,
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48 parser: Optional[Parser] = ...,
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49 multiple_iterators: bool = ...,
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50 ) -> Any: ...
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51 def close(self) -> None: ...
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52
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53 class TabixIterator:
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54 def __init__(self, encoding: str = ...) -> None: ...
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55 def __iter__(self) -> TabixIterator: ...
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56 def __next__(self) -> str: ...
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57
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58 class EmptyIterator:
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59 def __iter__(self) -> Any: ...
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60 def __next__(self) -> Any: ...
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61
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62 class TabixIteratorParsed(TabixIterator):
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63 def __init__(self, parser: Parser) -> None: ...
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64 def __next__(self) -> Any: ...
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65
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66 class GZIterator:
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67 def __init__(
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68 self, filename: str, bufer_size: int = ..., encoding: str = ...
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69 ) -> None: ...
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70 def __iter__(self) -> GZIterator: ...
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71 def __next__(self) -> str: ...
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72
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73 class GZIteratorHead(GZIterator): ...
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74
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75 class GZIteratorParsed(GZIterator):
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76 def __init__(self, parser: Parser) -> None: ...
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77 def __next__(self) -> _ParseResult: ...
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78
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79 def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ...
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80 def tabix_index(
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81 filename: str,
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82 force: bool = ...,
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83 seq_col: Optional[int] = ...,
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84 start_col: Optional[int] = ...,
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85 end_col: Optional[int] = ...,
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86 preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ...,
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87 meta_char: str = ...,
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88 line_skip: int = ...,
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89 zerobased: bool = ...,
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90 min_shift: int = ...,
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91 index: Optional[str] = ...,
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92 keep_original: bool = ...,
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93 csi: bool = ...,
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94 ) -> str: ...
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95
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96 class tabix_file_iterator:
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97 def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ...
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98 def __iter__(self) -> tabix_file_iterator: ...
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99 def __next__(self) -> _ParseResult: ...
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100
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101 class tabix_generic_iterator:
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102 def __init__(self, infile: str, parser: Parser) -> None: ...
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103 def __iter__(self) -> tabix_generic_iterator: ...
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104 def __next__(self) -> _ParseResult: ...
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105
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106 def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ...
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107
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108 # backwards compatibility
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109 class Tabixfile(TabixFile): ...
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