Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcalignedsegment.pyi @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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jpayne@69 1 import enum
jpayne@69 2 import re
jpayne@69 3 import sys
jpayne@69 4 from array import array
jpayne@69 5 from typing import Any, List, Optional, Dict, Tuple, Union, overload
jpayne@69 6
jpayne@69 7 if sys.version_info < (3, 8):
jpayne@69 8 from typing_extensions import Literal
jpayne@69 9 else:
jpayne@69 10 from typing import Literal
jpayne@69 11
jpayne@69 12 from pysam import AlignmentHeader # type: ignore
jpayne@69 13
jpayne@69 14 CMATCH: int
jpayne@69 15 CINS: int
jpayne@69 16 CDEL: int
jpayne@69 17 CREF_SKIP: int
jpayne@69 18 CSOFT_CLIP: int
jpayne@69 19 CHARD_CLIP: int
jpayne@69 20 CPAD: int
jpayne@69 21 CEQUAL: int
jpayne@69 22 CDIFF: int
jpayne@69 23 CBACK: int
jpayne@69 24
jpayne@69 25 FPAIRED: int
jpayne@69 26 FPROPER_PAIR: int
jpayne@69 27 FUNMAP: int
jpayne@69 28 FMUNMAP: int
jpayne@69 29 FREVERSE: int
jpayne@69 30 FMREVERSE: int
jpayne@69 31 FREAD1: int
jpayne@69 32 FREAD2: int
jpayne@69 33 FSECONDARY: int
jpayne@69 34 FQCFAIL: int
jpayne@69 35 FDUP: int
jpayne@69 36 FSUPPLEMENTARY: int
jpayne@69 37
jpayne@69 38 CIGAR2CODE: Dict[int, str]
jpayne@69 39 CIGAR_REGEX: re.Pattern
jpayne@69 40 DATATYPE2FORMAT: Dict[int, Tuple[str, int]]
jpayne@69 41 KEY_NAMES: List[str]
jpayne@69 42
jpayne@69 43 TagValue = Union[str, int, float, array]
jpayne@69 44
jpayne@69 45 class CIGAR_OPS(enum.IntEnum):
jpayne@69 46 CBACK = ...
jpayne@69 47 CDEL = ...
jpayne@69 48 CDIFF = ...
jpayne@69 49 CEQUAL = ...
jpayne@69 50 CHARD_CLIP = ...
jpayne@69 51 CINS = ...
jpayne@69 52 CMATCH = ...
jpayne@69 53 CPAD = ...
jpayne@69 54 CREF_SKIP = ...
jpayne@69 55 CSOFT_CLIP = ...
jpayne@69 56
jpayne@69 57 class SAM_FLAGS(enum.IntEnum):
jpayne@69 58 FDUP = ...
jpayne@69 59 FMREVERSE = ...
jpayne@69 60 FMUNMAP = ...
jpayne@69 61 FPAIRED = ...
jpayne@69 62 FPROPER_PAIR = ...
jpayne@69 63 FQCFAIL = ...
jpayne@69 64 FREAD1 = ...
jpayne@69 65 FREAD2 = ...
jpayne@69 66 FREVERSE = ...
jpayne@69 67 FSECONDARY = ...
jpayne@69 68 FSUPPLEMENTARY = ...
jpayne@69 69 FUNMAP = ...
jpayne@69 70
jpayne@69 71 class AlignedSegment:
jpayne@69 72 header: AlignmentHeader
jpayne@69 73 query_name: Optional[str]
jpayne@69 74 flag: int
jpayne@69 75 reference_name: Optional[str]
jpayne@69 76 reference_id: int
jpayne@69 77 reference_start: int
jpayne@69 78 mapping_quality: int
jpayne@69 79 cigarstring: Optional[str]
jpayne@69 80 next_reference_id: int
jpayne@69 81 next_reference_name: Optional[str]
jpayne@69 82 next_reference_start: int
jpayne@69 83 template_length: int
jpayne@69 84 query_sequence: Optional[str]
jpayne@69 85 query_qualities: Optional[array]
jpayne@69 86 bin: int
jpayne@69 87 is_paired: bool
jpayne@69 88 is_proper_pair: bool
jpayne@69 89 is_unmapped: bool
jpayne@69 90 mate_is_unmapped: bool
jpayne@69 91 is_mapped: bool
jpayne@69 92 mate_is_mapped: bool
jpayne@69 93 is_reverse: bool
jpayne@69 94 mate_is_reverse: bool
jpayne@69 95 is_forward: bool
jpayne@69 96 mate_is_forward: bool
jpayne@69 97 is_read1: bool
jpayne@69 98 is_read2: bool
jpayne@69 99 is_secondary: bool
jpayne@69 100 is_qcfail: bool
jpayne@69 101 is_duplicate: bool
jpayne@69 102 is_supplementary: bool
jpayne@69 103 cigartuples: Optional[List[Tuple[int, int]]]
jpayne@69 104 def __init__(self, header: Optional[AlignmentHeader] = ...) -> None: ...
jpayne@69 105 def compare(self, other: Any) -> int: ...
jpayne@69 106 def to_string(self) -> str: ...
jpayne@69 107 @classmethod
jpayne@69 108 def fromstring(cls, sam: str, header: AlignmentHeader) -> AlignedSegment: ...
jpayne@69 109 def to_dict(self) -> Dict: ...
jpayne@69 110 @classmethod
jpayne@69 111 def from_dict(cls, sam_dict: Dict[str, Any], header: AlignmentHeader) -> Any: ...
jpayne@69 112 def get_reference_positions(self, full_length: bool = ...) -> List[int]: ...
jpayne@69 113 @property
jpayne@69 114 def query_length(self) -> int: ...
jpayne@69 115 @property
jpayne@69 116 def reference_end(self) -> Optional[int]: ...
jpayne@69 117 @property
jpayne@69 118 def reference_length(self) -> Optional[int]: ...
jpayne@69 119 @property
jpayne@69 120 def query_alignment_sequence(self) -> Optional[str]: ...
jpayne@69 121 @property
jpayne@69 122 def query_alignment_qualities(self) -> Optional[array]: ...
jpayne@69 123 @property
jpayne@69 124 def query_alignment_start(self) -> int: ...
jpayne@69 125 @property
jpayne@69 126 def query_alignment_end(self) -> int: ...
jpayne@69 127 @property
jpayne@69 128 def modified_bases(self) -> Optional[Dict[Tuple[str, int, str], List[Tuple[int, int]]]]: ...
jpayne@69 129 @property
jpayne@69 130 def modified_bases_forward(self) -> Optional[Dict[Tuple[str, int, str], List[Tuple[int, int]]]]: ...
jpayne@69 131 @property
jpayne@69 132 def query_alignment_length(self) -> int: ...
jpayne@69 133 def infer_query_length(self) -> Optional[int]: ...
jpayne@69 134 def infer_read_length(self) -> Optional[int]: ...
jpayne@69 135 def get_reference_sequence(self) -> str: ...
jpayne@69 136 def get_forward_sequence(self) -> Optional[str]: ...
jpayne@69 137 def get_forward_qualities(self) -> Optional[array]: ...
jpayne@69 138 def get_aligned_pairs(
jpayne@69 139 self, matches_only: bool = ..., with_seq: bool = ..., with_cigar: bool = ...
jpayne@69 140 ) -> List[Tuple[int, int]]: ...
jpayne@69 141 def get_blocks(self) -> List[Tuple[int, int]]: ...
jpayne@69 142 def get_overlap(self, start: int, end: int) -> Optional[int]: ...
jpayne@69 143 def get_cigar_stats(self) -> Tuple[array, array]: ...
jpayne@69 144 def set_tag(
jpayne@69 145 self,
jpayne@69 146 tag: str,
jpayne@69 147 value: Union[int, float, str, bytes, array, List, Tuple, None],
jpayne@69 148 value_type: Optional[
jpayne@69 149 Literal["A", "i", "f", "Z", "H", "B", "c", "C", "s", "S", "I"]
jpayne@69 150 ] = ...,
jpayne@69 151 replace: bool = ...,
jpayne@69 152 ) -> None: ...
jpayne@69 153 def has_tag(self, tag: str) -> bool: ...
jpayne@69 154 @overload
jpayne@69 155 def get_tag(self, tag: str, with_value_type: Literal[False] = ...) -> TagValue: ...
jpayne@69 156 @overload
jpayne@69 157 def get_tag(
jpayne@69 158 self, tag: str, with_value_type: Literal[True]
jpayne@69 159 ) -> Tuple[TagValue, str]: ...
jpayne@69 160 @overload
jpayne@69 161 def get_tag(
jpayne@69 162 self, tag: str, with_value_type: bool
jpayne@69 163 ) -> Union[TagValue, Tuple[TagValue, str]]: ...
jpayne@69 164 @overload
jpayne@69 165 def get_tags(
jpayne@69 166 self, with_value_type: Literal[False] = ...
jpayne@69 167 ) -> List[Tuple[str, TagValue]]: ...
jpayne@69 168 @overload
jpayne@69 169 def get_tags(
jpayne@69 170 self, with_value_type: Literal[True]
jpayne@69 171 ) -> List[Tuple[str, TagValue, str]]: ...
jpayne@69 172 @overload
jpayne@69 173 def get_tags(
jpayne@69 174 self, with_value_type: bool
jpayne@69 175 ) -> Union[List[Tuple[str, TagValue]], List[Tuple[str, TagValue, str]]]: ...
jpayne@69 176 @overload
jpayne@69 177 def get_tags(
jpayne@69 178 self, with_value_type: bool = ...
jpayne@69 179 ) -> Union[List[Tuple[str, TagValue, str]], List[Tuple[str, TagValue]]]: ...
jpayne@69 180 def set_tags(self, tags: Any) -> None: ...
jpayne@69 181 def __eq__(self, other): ...
jpayne@69 182 def __ge__(self, other): ...
jpayne@69 183 def __gt__(self, other): ...
jpayne@69 184 def __le__(self, other): ...
jpayne@69 185 def __lt__(self, other): ...
jpayne@69 186 def __ne__(self, other): ...
jpayne@69 187
jpayne@69 188 class PileupRead:
jpayne@69 189 @property
jpayne@69 190 def alignment(self) -> AlignedSegment: ...
jpayne@69 191 @property
jpayne@69 192 def query_position(self) -> Optional[int]: ...
jpayne@69 193 @property
jpayne@69 194 def query_position_or_next(self) -> int: ...
jpayne@69 195 @property
jpayne@69 196 def indel(self) -> int: ...
jpayne@69 197 @property
jpayne@69 198 def level(self) -> int: ...
jpayne@69 199 @property
jpayne@69 200 def is_del(self) -> int: ...
jpayne@69 201 @property
jpayne@69 202 def is_head(self) -> int: ...
jpayne@69 203 @property
jpayne@69 204 def is_tail(self) -> int: ...
jpayne@69 205 @property
jpayne@69 206 def is_refskip(self) -> int: ...
jpayne@69 207
jpayne@69 208 class PileupColumn:
jpayne@69 209 nsegments: int
jpayne@69 210 def set_min_base_quality(self, min_base_quality: int) -> None: ...
jpayne@69 211 def __len__(self) -> int: ...
jpayne@69 212 @property
jpayne@69 213 def reference_id(self) -> int: ...
jpayne@69 214 @property
jpayne@69 215 def reference_name(self) -> Optional[str]: ...
jpayne@69 216 @property
jpayne@69 217 def reference_pos(self) -> int: ...
jpayne@69 218 @property
jpayne@69 219 def pileups(self) -> List[PileupRead]: ...
jpayne@69 220 def get_num_aligned(self) -> int: ...
jpayne@69 221 def get_query_sequences(
jpayne@69 222 self,
jpayne@69 223 mark_matches: bool = ...,
jpayne@69 224 mark_ends: bool = ...,
jpayne@69 225 add_indels: bool = ...,
jpayne@69 226 ) -> List[str]: ...
jpayne@69 227 def get_query_qualities(self) -> List[int]: ...
jpayne@69 228 def get_mapping_qualities(self) -> List[int]: ...
jpayne@69 229 def get_query_positions(self) -> List[int]: ...
jpayne@69 230 def get_query_names(self) -> List[str]: ...