Skip to content

Commit 2a5e55e

Browse files
AndreasHegerAndreasHeger
authored
Merge pull request #1008 from marcelm/type-hints
Start adding type hints
2 parents d94fe42 + 83e4873 commit 2a5e55e

19 files changed

+1269
-20
lines changed

‎pysam/Pileup.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
import pysam
44

55
PileupSubstitution = collections.namedtuple("PileupSubstitution",
6-
" ".join((
6+
(
77
"chromosome",
88
"pos",
99
"reference_base",
@@ -13,10 +13,10 @@
1313
"mapping_quality",
1414
"coverage",
1515
"read_bases",
16-
"base_qualities")))
16+
"base_qualities"))
1717

1818
PileupIndel = collections.namedtuple("PileupIndel",
19-
" ".join((
19+
(
2020
"chromosome",
2121
"pos",
2222
"reference_base",
@@ -29,7 +29,7 @@
2929
"second_allele",
3030
"reads_first",
3131
"reads_second",
32-
"reads_diff")))
32+
"reads_diff"))
3333

3434

3535
def iterate(infile):

‎pysam/__init__.py‎

Lines changed: 15 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@
22
import sysconfig
33

44
from pysam.libchtslib import *
5+
import pysam.libchtslib as libchtslib
56
from pysam.libcsamtools import *
67
from pysam.libcbcftools import *
78
from pysam.libcutils import *
@@ -31,21 +32,21 @@
3132

3233

3334
# export all the symbols from separate modules
34-
__all__ = \
35-
libchtslib.__all__ +\
36-
libcutils.__all__ +\
37-
libctabix.__all__ +\
38-
libcvcf.__all__ +\
39-
libcbcf.__all__ +\
40-
libcbgzf.__all__ +\
41-
libcfaidx.__all__ +\
42-
libctabixproxies.__all__ +\
43-
libcalignmentfile.__all__ +\
44-
libcalignedsegment.__all__ +\
45-
libcsamfile.__all__ +\
46-
["SamtoolsError"] +\
35+
__all__ = (
36+
libchtslib.__all__ + # type: ignore
37+
libcutils.__all__ + # type: ignore
38+
libctabix.__all__ + # type: ignore
39+
libcvcf.__all__ + # type: ignore
40+
libcbcf.__all__ + # type: ignore
41+
libcbgzf.__all__ + # type: ignore
42+
libcfaidx.__all__ + # type: ignore
43+
libctabixproxies.__all__ + # type: ignore
44+
libcalignmentfile.__all__ + # type: ignore
45+
libcalignedsegment.__all__ + # type: ignore
46+
libcsamfile.__all__ + # type: ignore
47+
["SamtoolsError"] +
4748
["Pileup"]
48-
49+
)
4950
from pysam.version import __version__, __samtools_version__
5051

5152

‎pysam/libcalignedsegment.pyi‎

Lines changed: 216 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,216 @@
1+
import enum
2+
import re
3+
import sys
4+
from array import array
5+
from typing import Any, List, Optional, Dict, Tuple, Union, overload
6+
7+
if sys.version_info < (3, 8):
8+
from typing_extensions import Literal
9+
else:
10+
from typing import Literal
11+
12+
from pysam import AlignmentHeader # type: ignore
13+
14+
CMATCH: int
15+
CINS: int
16+
CDEL: int
17+
CREF_SKIP: int
18+
CSOFT_CLIP: int
19+
CHARD_CLIP: int
20+
CPAD: int
21+
CEQUAL: int
22+
CDIFF: int
23+
CBACK: int
24+
25+
FPAIRED: int
26+
FPROPER_PAIR: int
27+
FUNMAP: int
28+
FMUNMAP: int
29+
FREVERSE: int
30+
FMREVERSE: int
31+
FREAD1: int
32+
FREAD2: int
33+
FSECONDARY: int
34+
FQCFAIL: int
35+
FDUP: int
36+
FSUPPLEMENTARY: int
37+
38+
CIGAR2CODE: Dict[int, str]
39+
CIGAR_REGEX: re.Pattern
40+
DATATYPE2FORMAT: Dict[int, Tuple[str, int]]
41+
KEY_NAMES: List[str]
42+
43+
TagValue = Union[str, int, float, array]
44+
45+
class CIGAR_OPS(enum.IntEnum):
46+
CBACK: int
47+
CDEL: int
48+
CDIFF: int
49+
CEQUAL: int
50+
CHARD_CLIP: int
51+
CINS: int
52+
CMATCH: int
53+
CPAD: int
54+
CREF_SKIP: int
55+
CSOFT_CLIP: int
56+
57+
class SAM_FLAGS(enum.IntEnum):
58+
FDUP: int
59+
FMREVERSE: int
60+
FMUNMAP: int
61+
FPAIRED: int
62+
FPROPER_PAIR: int
63+
FQCFAIL: int
64+
FREAD1: int
65+
FREAD2: int
66+
FREVERSE: int
67+
FSECONDARY: int
68+
FSUPPLEMENTARY: int
69+
FUNMAP: int
70+
71+
class AlignedSegment:
72+
header: AlignmentHeader
73+
query_name: Optional[str]
74+
flag: int
75+
reference_name: Optional[str]
76+
reference_id: int
77+
reference_start: int
78+
mapping_quality: int
79+
cigarstring: Optional[str]
80+
next_reference_id: int
81+
next_reference_name: Optional[str]
82+
next_reference_start: int
83+
template_length: int
84+
query_sequence: Optional[str]
85+
query_qualities: Optional[array]
86+
bin: int
87+
is_paired: bool
88+
is_proper_pair: bool
89+
is_unmapped: bool
90+
mate_is_unmapped: bool
91+
is_reverse: bool
92+
mate_is_reverse: bool
93+
is_read1: bool
94+
is_read2: bool
95+
is_secondary: bool
96+
is_qcfail: bool
97+
is_duplicate: bool
98+
is_supplementary: bool
99+
cigartuples: Optional[List[Tuple[int, int]]]
100+
def __init__(self, header: Optional[AlignmentHeader] = ...) -> None: ...
101+
def compare(self, other: Any) -> int: ...
102+
def to_string(self) -> str: ...
103+
@classmethod
104+
def fromstring(cls, sam: str, header: AlignmentHeader) -> AlignedSegment: ...
105+
def to_dict(self) -> Dict: ...
106+
@classmethod
107+
def from_dict(cls, sam_dict: Dict[str, Any], header: AlignmentHeader) -> Any: ...
108+
def get_reference_positions(self, full_length: bool = ...) -> List[int]: ...
109+
@property
110+
def query_length(self) -> int: ...
111+
@property
112+
def reference_end(self) -> Optional[int]: ...
113+
@property
114+
def reference_length(self) -> Optional[int]: ...
115+
@property
116+
def query_alignment_sequence(self) -> Optional[str]: ...
117+
@property
118+
def query_alignment_qualities(self) -> Optional[array]: ...
119+
@property
120+
def query_alignment_start(self) -> int: ...
121+
@property
122+
def query_alignment_end(self) -> int: ...
123+
@property
124+
def query_alignment_length(self) -> int: ...
125+
def infer_query_length(self) -> Optional[int]: ...
126+
def infer_read_length(self) -> Optional[int]: ...
127+
def get_reference_sequence(self) -> str: ...
128+
def get_forward_sequence(self) -> Optional[str]: ...
129+
def get_forward_qualities(self) -> Optional[array]: ...
130+
def get_aligned_pairs(
131+
self, matches_only: bool = ..., with_seq: bool = ...
132+
) -> List[Tuple[int, int]]: ...
133+
def get_blocks(self) -> List[Tuple[int, int]]: ...
134+
def get_overlap(self, start: int, end: int) -> Optional[int]: ...
135+
def get_cigar_stats(self) -> Tuple[array, array]: ...
136+
def set_tag(
137+
self,
138+
tag: str,
139+
value: Union[int, float, str, bytes, array, List, Tuple, None],
140+
value_type: Optional[
141+
Literal["A", "i", "f", "Z", "H", "B", "c", "C", "s", "S", "I"]
142+
] = ...,
143+
replace: bool = ...,
144+
) -> None: ...
145+
def has_tag(self, tag: str) -> bool: ...
146+
@overload
147+
def get_tag(self, tag: str, with_value_type: Literal[False]) -> TagValue: ...
148+
@overload
149+
def get_tag(self, tag, with_value_type: Literal[True]) -> Tuple[TagValue, str]: ...
150+
@overload
151+
def get_tag(
152+
self, tag, with_value_type: bool = ...
153+
) -> Union[TagValue, Tuple[TagValue, str]]: ...
154+
@overload
155+
def get_tags(
156+
self, with_value_type: Literal[False]
157+
) -> List[Tuple[str, TagValue]]: ...
158+
@overload
159+
def get_tags(
160+
self, with_value_type: Literal[True]
161+
) -> List[Tuple[str, TagValue, str]]: ...
162+
@overload
163+
def get_tags(
164+
self, with_value_type: bool = ...
165+
) -> Union[List[Tuple[str, TagValue, str]], List[Tuple[str, TagValue]]]: ...
166+
def set_tags(self, tags: Any) -> None: ...
167+
def __eq__(self, other): ...
168+
def __ge__(self, other): ...
169+
def __gt__(self, other): ...
170+
def __le__(self, other): ...
171+
def __lt__(self, other): ...
172+
def __ne__(self, other): ...
173+
174+
class PileupRead:
175+
@property
176+
def alignment(self) -> AlignedSegment: ...
177+
@property
178+
def query_position(self) -> Optional[int]: ...
179+
@property
180+
def query_position_or_next(self) -> int: ...
181+
@property
182+
def indel(self) -> int: ...
183+
@property
184+
def level(self) -> int: ...
185+
@property
186+
def is_del(self) -> int: ...
187+
@property
188+
def is_head(self) -> int: ...
189+
@property
190+
def is_tail(self) -> int: ...
191+
@property
192+
def is_refskip(self) -> int: ...
193+
194+
class PileupColumn:
195+
nsegments: int
196+
def set_min_base_quality(self, min_base_quality: int) -> None: ...
197+
def __len__(self) -> int: ...
198+
@property
199+
def reference_id(self) -> int: ...
200+
@property
201+
def reference_name(self) -> Optional[str]: ...
202+
@property
203+
def reference_pos(self) -> int: ...
204+
@property
205+
def pileups(self) -> List[PileupRead]: ...
206+
def get_num_aligned(self) -> int: ...
207+
def get_query_sequences(
208+
self,
209+
mark_matches: bool = ...,
210+
mark_ends: bool = ...,
211+
add_indels: bool = ...,
212+
) -> List[str]: ...
213+
def get_query_qualities(self) -> List[int]: ...
214+
def get_mapping_qualities(self) -> List[int]: ...
215+
def get_query_positions(self) -> List[int]: ...
216+
def get_query_names(self) -> List[str]: ...

0 commit comments

Comments
 (0)