twitcher 0.7.0

Find template switch mutations in genomic data
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[package]
name = "twitcher"
version = "0.7.0"
authors = ["Jasper Krauter <jasper.krauter@helsinki.fi>"]
edition = "2024"
rust-version = "1.96.0"
description = "Find template switch mutations in genomic data"
documentation = "https://docs.rs/twitcher"
readme = "../README.md"
repository = "https://version.helsinki.fi/kraujasp/twitcher"
license = "MIT"
keywords = ["htslib", "mutations", "genome", "bioinformatics"]

[dependencies]
anyhow = "1"
bytesize = "2"
clap = { version = "4", features = ["derive"] }
clap-verbosity-flag = { version = "3", default-features = false, features = ["tracing", "serde"] }
generic_a_star = { version = "5", features = ["serde"] }
indicatif = "0.18"
lib_tsalign = { version = "5", features = ["serde"] }
lib_tsshow = { version = "5" }
rust-htslib.workspace = true
sysinfo = "0.38"
tracing = "0.1"
tracing-indicatif = "0.3"
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
url = "2"
bstr = "1"
bitvec = "1"
regex = "1"
csv = "1"
serde = { version = "1", features = ["derive", "rc"] }
itertools = "0.15"
compact-genome = "12"
rmp-serde = "1"
rlimit = "0.11"
tokio = { version = "1", features = ["rt-multi-thread", "io-util", "io-std", "time", "process", "macros", "fs"] }
tokio-stream = "0.1"
async-stream = "0.3"
rusqlite = { version = "0.39", features = ["bundled"] }
xxhash-rust = { version = "0.8.15", features = ["xxh3"] }

[dev-dependencies]
assert_cmd = "2"
tempfile = "3"

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

[lints.clippy]
pedantic = { level = "warn", priority = -1 }
# nursery = { level = "warn", priority = -1 }

tuple_array_conversions = "allow" # Code style
option_if_let_else = "allow" # Code style
significant_drop_tightening = "allow" # Too many false positives

print_stdout = "deny"
print_stderr = "deny"
todo = "deny"
unimplemented = "warn"
dbg_macro = "warn"
mem_forget = "deny"
future_not_send = "warn"
redundant_clone = "warn"
inefficient_to_string = "warn"
let_underscore_future = "warn"
unused_async = "warn"
rc_buffer = "warn"
large_stack_frames = "warn"
verbose_file_reads = "warn"
assigning_clones = "warn"

unwrap_used = "warn"
expect_used = "warn"
indexing_slicing = "warn"
unreachable = "warn"
unchecked_time_subtraction = "warn"
string_slice = "warn"
panic = "warn"
exit = "warn"