perbase 1.3.0

Fast and correct perbase BAM/CRAM analysis.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
# with all versions of Cargo and also rewrite `path` dependencies
# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
# will likely look very different (and much more reasonable).
# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
name = "perbase"
version = "1.3.0"
authors = ["Seth Stadick <sstadick@gmail.com>"]
build = false
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Fast and correct perbase BAM/CRAM analysis."
documentation = "https://docs.rs/perbase"
readme = "README.md"
keywords = [
    "depth",
    "coverage",
    "bioinformatics",
    "genomic",
]
categories = ["science"]
license = "MIT"
repository = "https://github.com/sstadick/perbase"

[lib]
name = "perbase_lib"
path = "src/lib/mod.rs"

[[bin]]
name = "perbase"
path = "src/main.rs"

[[example]]
name = "par_granges_example"
path = "examples/par_granges_example.rs"

[dependencies.anyhow]
version = "1.0.41"

[dependencies.bio]
version = "3.0.0"

[dependencies.crossbeam]
version = "0.8"

[dependencies.crossbeam-channel]
version = "0.5"

[dependencies.csv]
version = "1.1.6"

[dependencies.env_logger]
version = "0.11.8"

[dependencies.grep-cli]
version = "0.1.5"

[dependencies.gzp]
version = "2.0"

[dependencies.itertools]
version = "0.14.0"

[dependencies.lazy_static]
version = "1.4.0"

[dependencies.log]
version = "0.4.11"

[dependencies.lru_time_cache]
version = "0.11.1"

[dependencies.num_cpus]
version = "1.13.0"

[dependencies.rayon]
version = "1.4.0"

[dependencies.rust-htslib]
version = "0.51"
features = ["libdeflate"]
default-features = false

[dependencies.rust-lapper]
version = "1.0"

[dependencies.serde]
version = "1.0.116"
features = ["derive"]

[dependencies.smartstring]
version = "1.0.1"
features = ["serde"]

[dependencies.structopt]
version = "0.3.18"

[dependencies.strum]
version = "0.27.1"
features = ["derive"]

[dependencies.termcolor]
version = "1.1.0"

[dev-dependencies.proptest]
version = "1.0.0"

[dev-dependencies.rstest]
version = "0.26.1"

[dev-dependencies.tempfile]
version = "3.1.0"

[profile.release]
lto = "fat"
codegen-units = 1