seqair 0.1.0

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
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#
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# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
rust-version = "1.92.0"
name = "seqair"
version = "0.1.0"
build = false
exclude = [
    "fuzz/*",
    "tests/*",
    "benches/*",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Pure-Rust BAM/SAM/CRAM/FASTA reader and pileup engine"
readme = "README.md"
license = "MIT OR Apache-2.0"
repository = "https://github.com/Softleif/seqair"
resolver = "2"

[package.metadata.docs.rs]
cargo-args = [
    "-Zunstable-options",
    "-Zrustdoc-scrape-examples",
]

[features]
fuzz = []

[lib]
name = "seqair"
path = "src/lib.rs"

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

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

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

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

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

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

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

[dependencies.bytemuck]
version = "1.25"
features = ["derive"]

[dependencies.bzip2]
version = "0.6.1"

[dependencies.flate2]
version = "1.1.9"

[dependencies.indexmap]
version = "2"

[dependencies.itoa]
version = "1"

[dependencies.libdeflater]
version = "1.25.2"

[dependencies.md5]
version = "0.8.0"

[dependencies.rustc-hash]
version = "2.1.2"

[dependencies.ryu]
version = "1"

[dependencies.seqair-types]
version = "^0.1.0"

[dependencies.thiserror]
version = "2.0.18"

[dependencies.tracing]
version = "0.1.44"
features = ["release_max_level_debug"]

[dependencies.xz2]
version = "0.1.7"

[dev-dependencies.anyhow]
version = "1.0.102"

[dev-dependencies.bgzf]
version = "0.3.0"

[dev-dependencies.clap]
version = "4.6.1"
features = ["derive"]

[dev-dependencies.criterion]
version = "0.8"
features = ["html_reports"]

[dev-dependencies.cstr8]
version = "0.1.4"

[dev-dependencies.insta]
version = "1.47.2"
features = ["filters"]

[dev-dependencies.noodles]
version = "0.110.0"
features = [
    "bam",
    "bcf",
    "bgzf",
    "core",
    "cram",
    "fasta",
    "sam",
    "vcf",
]

[dev-dependencies.noodles-bgzf]
version = "0.47.0"
features = ["libdeflate"]

[dev-dependencies.noodles-util]
version = "0.79.0"
features = ["alignment"]

[dev-dependencies.proptest]
version = "1.11.0"

[dev-dependencies.rust-htslib]
version = "1.0.0"
features = [
    "libdeflate",
    "bzip2",
    "lzma",
    "static",
]
default-features = false

[dev-dependencies.tempfile]
version = "3.27.0"

[lints.clippy]
allow_attributes_without_reason = "warn"
arithmetic_side_effects = "warn"
cast_lossless = "warn"
cast_possible_truncation = "warn"
cast_possible_wrap = "warn"
comparison_chain = "warn"
create_dir = "warn"
dbg_macro = "warn"
default_trait_access = "warn"
doc_link_with_quotes = "warn"
doc_markdown = "warn"
equatable_if_let = "warn"
explicit_into_iter_loop = "warn"
format_collect = "warn"
format_in_format_args = "warn"
format_push_string = "warn"
implicit_clone = "warn"
index_refutable_slice = "warn"
indexing_slicing = "warn"
inefficient_to_string = "warn"
infinite_loop = "warn"
lossy_float_literal = "warn"
manual_assert = "warn"
manual_is_variant_and = "warn"
manual_let_else = "warn"
manual_string_new = "warn"
mem_forget = "warn"
non_zero_suggestions = "warn"
ok_expect = "warn"
option_option = "warn"
panic = "deny"
pathbuf_init_then_push = "warn"
print_stdout = "warn"
range_minus_one = "warn"
range_plus_one = "warn"
rc_buffer = "warn"
return_and_then = "warn"
same_name_method = "warn"
undocumented_unsafe_blocks = "deny"
unwrap_in_result = "warn"
unwrap_used = "warn"

[lints.rust.unexpected_cfgs]
level = "warn"
priority = 0
check-cfg = ["cfg(coverage, coverage_nightly)"]