methylsieve 0.1.0

Fast per-template tagging and filtering of unconverted reads in bisulfite / EM-seq SAM/BAM files
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# 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"
rust-version = "1.94"
name = "methylsieve"
version = "0.1.0"
authors = ["Tim Fennell <tim@fulcrumgenomics.com>"]
build = false
exclude = [
    "/benchmark-pipeline",
    "/dev",
    "/docs",
    "/.github",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Fast per-template tagging and filtering of unconverted reads in bisulfite / EM-seq SAM/BAM files"
homepage = "https://github.com/fulcrumgenomics/methylsieve"
readme = "README.md"
keywords = [
    "bioinformatics",
    "genomics",
    "bisulfite",
    "methylation",
    "bam",
]
categories = [
    "science::bioinformatics",
    "command-line-utilities",
]
license = "MIT"
repository = "https://github.com/fulcrumgenomics/methylsieve"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[dependencies.anyhow]
version = "1"

[dependencies.bgzf]
version = "0.3.0"

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

[dependencies.env_logger]
version = "0.11"

[dependencies.fgumi-raw-bam]
version = "0.2.0"

[dependencies.libc]
version = "0.2"

[dependencies.libdeflater]
version = "1.25"

[dependencies.log]
version = "0.4"

[dependencies.memchr]
version = "2"

[dependencies.mimalloc]
version = "0.1"
default-features = false

[dependencies.noodles-core]
version = "0.20"

[dependencies.noodles-fasta]
version = "0.62"

[dependencies.noodles-sam]
version = "0.85"

[dependencies.ringbuf]
version = "0.5"

[dependencies.wide]
version = "1.4"

[dev-dependencies.noodles-bam]
version = "0.90"

[dev-dependencies.noodles-util]
version = "0.80"
features = ["alignment"]

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

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