twitcher 0.7.0

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
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# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
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#
# 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"
rust-version = "1.96.0"
name = "twitcher"
version = "0.7.0"
authors = ["Jasper Krauter <jasper.krauter@helsinki.fi>"]
build = false
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Find template switch mutations in genomic data"
documentation = "https://docs.rs/twitcher"
readme = "README.md"
keywords = [
    "htslib",
    "mutations",
    "genome",
    "bioinformatics",
]
license = "MIT"
repository = "https://version.helsinki.fi/kraujasp/twitcher"

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

[[test]]
name = "reads_tests"
path = "tests/reads_tests.rs"

[[test]]
name = "vcf_tests"
path = "tests/vcf_tests.rs"

[[test]]
name = "viz_tests"
path = "tests/viz_tests.rs"

[dependencies.anyhow]
version = "1"

[dependencies.async-stream]
version = "0.3"

[dependencies.bitvec]
version = "1"

[dependencies.bstr]
version = "1"

[dependencies.bytesize]
version = "2"

[dependencies.clap]
version = "4"
features = ["derive"]

[dependencies.clap-verbosity-flag]
version = "3"
features = [
    "tracing",
    "serde",
]
default-features = false

[dependencies.compact-genome]
version = "12"

[dependencies.csv]
version = "1"

[dependencies.generic_a_star]
version = "5"
features = ["serde"]

[dependencies.indicatif]
version = "0.18"

[dependencies.itertools]
version = "0.15"

[dependencies.lib_tsalign]
version = "5"
features = ["serde"]

[dependencies.lib_tsshow]
version = "5"

[dependencies.regex]
version = "1"

[dependencies.rlimit]
version = "0.11"

[dependencies.rmp-serde]
version = "1"

[dependencies.rusqlite]
version = "0.39"
features = ["bundled"]

[dependencies.rust-htslib]
version = "1"

[dependencies.serde]
version = "1"
features = [
    "derive",
    "rc",
]

[dependencies.sysinfo]
version = "0.38"

[dependencies.tokio]
version = "1"
features = [
    "rt-multi-thread",
    "io-util",
    "io-std",
    "time",
    "process",
    "macros",
    "fs",
]

[dependencies.tokio-stream]
version = "0.1"

[dependencies.tracing]
version = "0.1"

[dependencies.tracing-indicatif]
version = "0.3"

[dependencies.tracing-subscriber]
version = "0.3"
features = ["env-filter"]

[dependencies.url]
version = "2"

[dependencies.xxhash-rust]
version = "0.8.15"
features = ["xxh3"]

[dev-dependencies.assert_cmd]
version = "2"

[dev-dependencies.tempfile]
version = "3"

[lints.clippy]
assigning_clones = "warn"
dbg_macro = "warn"
exit = "warn"
expect_used = "warn"
future_not_send = "warn"
indexing_slicing = "warn"
inefficient_to_string = "warn"
large_stack_frames = "warn"
let_underscore_future = "warn"
mem_forget = "deny"
option_if_let_else = "allow"
panic = "warn"
print_stderr = "deny"
print_stdout = "deny"
rc_buffer = "warn"
redundant_clone = "warn"
significant_drop_tightening = "allow"
string_slice = "warn"
todo = "deny"
tuple_array_conversions = "allow"
unchecked_time_subtraction = "warn"
unimplemented = "warn"
unreachable = "warn"
unused_async = "warn"
unwrap_used = "warn"
verbose_file_reads = "warn"

[lints.clippy.pedantic]
level = "warn"
priority = -1

[lints.rust]
unsafe_code = "forbid"
unused_qualifications = "warn"