# 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 = "2021"
rust-version = "1.93"
name = "cyanea-io"
version = "0.1.0"
build = false
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "File format parsing for the Cyanea bioinformatics ecosystem"
readme = "README.md"
keywords = [
    "bioinformatics",
    "vcf",
    "sam",
    "bam",
    "gff",
]
categories = [
    "science",
    "parser-implementations",
]
license = "Apache-2.0"
repository = "https://github.com/cyanea-io/cyanea"

[features]
abi = []
bam = [
    "sam",
    "dep:flate2",
]
bcf = [
    "vcf",
    "dep:flate2",
]
bed = ["dep:cyanea-omics"]
bedgraph = []
bigwig = ["dep:flate2"]
blast = []
blast-xml = []
clustal = []
cram = [
    "sam",
    "dep:noodles-cram",
    "dep:noodles-sam",
    "dep:noodles-fasta",
    "dep:noodles-core",
]
csv = [
    "dep:csv",
    "dep:serde",
    "dep:serde_json",
]
default = ["csv"]
embl = []
fetch = []
genbank = []
gfa = []
gff = ["dep:cyanea-omics"]
gtf = ["dep:cyanea-omics"]
indexed = [
    "indexed-bam",
    "indexed-vcf",
]
indexed-bam = [
    "bam",
    "dep:noodles-bam",
    "dep:noodles-bgzf",
    "dep:noodles-sam",
    "dep:noodles-core",
    "dep:noodles-csi",
]
indexed-vcf = [
    "vcf",
    "dep:noodles-bgzf",
    "dep:noodles-csi",
    "dep:noodles-vcf",
    "dep:noodles-tabix",
    "dep:noodles-core",
]
maf = []
parallel = ["dep:rayon"]
parquet = [
    "dep:parquet",
    "dep:arrow",
    "vcf",
    "bed",
]
phylip = []
pir = []
sam = []
stockholm = []
variant-calling = [
    "sam",
    "vcf",
    "dep:cyanea-stats",
]
vcf = ["dep:cyanea-omics"]
wasm = []

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

[dependencies.arrow]
version = "54"
features = ["prettyprint"]
optional = true
default-features = false

[dependencies.csv]
version = "1.3"
optional = true

[dependencies.cyanea-core]
version = "0.1.0"
default-features = false

[dependencies.cyanea-omics]
version = "0.1.0"
optional = true
default-features = false

[dependencies.cyanea-stats]
version = "0.1.0"
optional = true
default-features = false

[dependencies.flate2]
version = "1.0"
optional = true

[dependencies.noodles-bam]
version = "0.71"
optional = true

[dependencies.noodles-bgzf]
version = "0.34"
optional = true

[dependencies.noodles-core]
version = "0.15"
optional = true

[dependencies.noodles-cram]
version = "0.72"
optional = true

[dependencies.noodles-csi]
version = "0.41"
optional = true

[dependencies.noodles-fasta]
version = "0.46"
optional = true

[dependencies.noodles-sam]
version = "0.67"
optional = true

[dependencies.noodles-tabix]
version = "0.47"
optional = true

[dependencies.noodles-vcf]
version = "0.70"
optional = true

[dependencies.parquet]
version = "54"
features = ["arrow"]
optional = true
default-features = false

[dependencies.rayon]
version = "1.10"
optional = true

[dependencies.serde]
version = "1.0"
features = ["derive"]
optional = true

[dependencies.serde_json]
version = "1.0"
optional = true

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