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1 import array
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2 import sys
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3 from typing import (
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4 Any,
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5 Dict,
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6 Type,
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7 NamedTuple,
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8 Tuple,
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9 Optional,
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10 Sequence,
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11 Union,
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12 Callable,
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13 List,
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14 Iterable,
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15 )
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16
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17 if sys.version_info < (3, 8):
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18 from typing_extensions import Literal
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19 else:
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20 from typing import Literal
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21
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22 from pysam.libchtslib import HTSFile, _HasFileNo
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23 from pysam.libcalignedsegment import AlignedSegment, PileupColumn
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24 from pysam.libcfaidx import FastaFile
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25
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26 class IndexStats(NamedTuple):
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27 contig: str
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28 mapped: int
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29 unmapped: int
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30 total: int
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31
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32 VALID_HEADER_TYPES: Dict[str, Type]
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33 VALID_HEADERS: Tuple[str]
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34 KNOWN_HEADER_FIELDS: Dict[str, Dict[str, Type]]
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35 VALID_HEADER_ORDER: Dict[str, Tuple[str]]
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36
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37 def build_header_line(fields: Dict[str, str], record: str) -> str: ...
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38
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39 class AlignmentHeader:
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40 def __init__(self) -> None: ...
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41 @classmethod
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42 def _from_text_and_lengths(
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43 cls,
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44 text: Optional[str],
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45 reference_names: Optional[Sequence[str]],
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46 reference_lengths: Optional[Sequence[int]],
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47 ) -> AlignmentHeader: ...
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48 @classmethod
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49 def from_text(cls, text: str) -> AlignmentHeader: ...
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50 @classmethod
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51 def from_dict(cls, header_dict: Dict) -> AlignmentHeader: ...
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52 @classmethod
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53 def from_references(
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54 cls,
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55 reference_names: Sequence[str],
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56 reference_lengths: Sequence[int],
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57 text: Optional[str] = ...,
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58 add_sq_text: bool = ...,
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59 ) -> AlignmentHeader: ...
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60 def __bool__(self) -> bool: ...
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61 def copy(self) -> AlignmentHeader: ...
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62 @property
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63 def nreferences(self) -> int: ...
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64 @property
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65 def references(self) -> Tuple[str]: ...
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66 @property
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67 def lengths(self) -> Tuple[int]: ...
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68 def to_dict(self) -> Dict: ...
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69 def get_reference_name(self, tid: int) -> Optional[str]: ...
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70 def get_reference_length(self, reference: str) -> int: ...
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71 def is_valid_tid(self, tid: int) -> bool: ...
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72 def get_tid(self, reference: str) -> int: ...
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73
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74 # The iterator produced by AlignmentFile is currently itself, but this may
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75 # change in future and code should not make assumptions about this type.
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76 AlignmentFileIterator = AlignmentFile
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77
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78 class AlignmentFile(HTSFile):
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79 def __init__(
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80 self,
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81 filename: Union[str, bytes, int, _HasFileNo],
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82 mode: Optional[
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83 Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0", "rc", "wc"]
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84 ] = ...,
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85 template: Optional[AlignmentFile] = ...,
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86 reference_names: Optional[Sequence[str]] = ...,
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87 reference_lengths: Optional[Sequence[int]] = ...,
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88 reference_filename: Optional[str] = ...,
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89 text: Optional[str] = ...,
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90 header: Union[None, Dict, AlignmentHeader] = ...,
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91 add_sq_text: bool = ...,
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92 add_sam_header: bool = ...,
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93 check_sq: bool = ...,
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94 index_filename: Optional[str] = ...,
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95 filepath_index: Optional[str] = ...,
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96 require_index: bool = ...,
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97 duplicate_filehandle: bool = ...,
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98 ignore_truncation: bool = ...,
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99 format_options: Optional[Sequence[str]] = ...,
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100 threads: int = ...,
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101 ) -> None: ...
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102 def has_index(self) -> bool: ...
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103 def check_index(self) -> bool: ...
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104 def fetch(
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105 self,
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106 contig: Optional[str] = ...,
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107 start: Optional[int] = ...,
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108 stop: Optional[int] = ...,
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109 region: Optional[str] = ...,
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110 tid: Optional[int] = ...,
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111 until_eof: bool = ...,
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112 multiple_iterators: bool = ...,
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113 reference: Optional[str] = ...,
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114 end: int = ...,
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115 ) -> IteratorRow: ...
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116 def head(self, n: int, multiple_iterators: bool = ...) -> IteratorRow: ...
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117 def mate(self, read: AlignedSegment) -> AlignedSegment: ...
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118 def pileup(
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119 self,
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120 contig: Optional[str] = ...,
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121 start: Optional[int] = ...,
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122 stop: Optional[int] = ...,
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123 region: Optional[str] = ...,
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124 reference: Optional[str] = ...,
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125 end: Optional[int] = ...,
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126 truncate: bool = ...,
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127 max_depth: int = ...,
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128 stepper: str = ...,
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129 fastafile: Optional[FastaFile] = ...,
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130 ignore_overlaps: bool = ...,
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131 flag_filter: int = ...,
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132 flag_require: int = ...,
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133 ignore_orphans: bool = ...,
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134 min_base_quality: int = ...,
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135 adjust_capq_threshold: int = ...,
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136 min_mapping_quality: int = ...,
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137 compute_baq: bool = ...,
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138 redo_baq: bool = ...,
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139 ) -> IteratorColumn: ...
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140 def count(
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141 self,
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142 contig: Optional[str] = ...,
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143 start: Optional[int] = ...,
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144 stop: Optional[int] = ...,
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145 region: Optional[str] = ...,
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146 until_eof: bool = ...,
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147 read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
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148 reference: Optional[str] = ...,
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149 end: Optional[int] = ...,
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150 ) -> int: ...
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151 def count_coverage(
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152 self,
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153 contig: Optional[str] = ...,
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154 start: Optional[int] = ...,
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155 stop: Optional[int] = ...,
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156 region: Optional[str] = ...,
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157 quality_threshold: int = ...,
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158 read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
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159 reference: Optional[str] = ...,
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160 end: Optional[int] = ...,
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161 ) -> Tuple[array.array, array.array, array.array, array.array]: ...
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162 def find_introns_slow(
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163 self, read_iterator: Iterable[AlignedSegment]
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164 ) -> Dict[Tuple[int, int], int]: ...
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165 def find_introns(
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166 self, read_iterator: Iterable[AlignedSegment]
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167 ) -> Dict[Tuple[int, int], int]: ...
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168 def close(self) -> None: ...
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169 def write(self, read: AlignedSegment) -> int: ...
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170 def __enter__(self) -> AlignmentFile: ...
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171 def __exit__(self, exc_type, exc_value, traceback): ...
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172 @property
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173 def mapped(self) -> int: ...
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174 @property
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175 def unmapped(self) -> int: ...
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176 @property
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177 def nocoordinate(self) -> int: ...
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178 def get_index_statistics(self) -> List[IndexStats]: ...
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179 def __iter__(self) -> AlignmentFileIterator: ...
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180 def __next__(self) -> AlignedSegment: ...
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181 def is_valid_tid(self, tid: int) -> bool: ...
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182 def get_tid(self, reference: str) -> int: ...
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183 def get_reference_name(self, tid: int) -> str: ...
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184 def get_reference_length(self, reference: str) -> int: ...
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185 @property
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186 def nreferences(self) -> int: ...
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187 @property
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188 def references(self) -> Tuple[str, ...]: ...
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189 @property
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190 def lengths(self) -> Tuple[int, ...]: ...
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191 @property
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192 def reference_filename(self) -> Optional[str]: ...
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193 @property
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194 def header(self) -> AlignmentHeader: ...
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195
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196 class IteratorRow:
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197 def __iter__(self) -> IteratorRow: ...
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198 def __next__(self) -> AlignedSegment: ...
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199
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200 class IteratorRowAll(IteratorRow): ...
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201 class IteratorRowAllRefs(IteratorRow): ...
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202 class IteratorRowHead(IteratorRow): ...
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203 class IteratorRowRegion(IteratorRow): ...
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204 class IteratorRowSelection(IteratorRow): ...
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205
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206 class IteratorColumn:
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207 def __iter__(self) -> IteratorColumn: ...
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208 def __next__(self) -> PileupColumn: ...
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209 @property
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210 def seq_len(self) -> int: ...
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211 def add_reference(self, fastafile: FastaFile) -> None: ...
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212 def has_reference(self) -> bool: ...
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213
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214 class IteratorColumnAll(IteratorColumn): ...
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215 class IteratorColumnAllRefs(IteratorColumn): ...
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216 class IteratorColumnRegion(IteratorColumn): ...
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217
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218 class SNPCall:
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219 @property
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220 def tid(self) -> int: ...
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221 @property
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222 def pos(self) -> int: ...
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223 @property
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224 def reference_base(self) -> str: ...
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225 @property
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226 def genotype(self) -> str: ...
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227 @property
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228 def consensus_quality(self) -> int: ...
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229 @property
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230 def snp_quality(self) -> int: ...
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231 @property
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232 def mapping_quality(self) -> int: ...
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233 @property
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234 def coverage(self) -> int: ...
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235
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236 class IndexedReads:
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237 def __init__(
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238 self, samfile: AlignmentFile, multiple_iterators: bool = ...
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239 ) -> None: ...
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240 def build(self) -> None: ...
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241 def find(self, query_name: str) -> IteratorRow: ...
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