feat: adds profile binary

.cargo/config.toml

@@ -0,0 +1,3 @@
+[profile.release-with-debug]
+inherits = "release"
+debug = true

.gitignore

@@ -7,3 +7,5 @@ target/
 rustc-ice*
 
 .idea
+
+flamegraph.svg

Cargo.toml

@@ -5,6 +5,7 @@ members = [
     "omics-core",
     "omics-molecule",
     "omics-variation",
+    "profile",
 ]
 resolver = "2"
 
@@ -21,6 +22,7 @@ rust-version = "1.80.0"
 anyhow = "1.0.89"
 criterion = "0.5.1"
 regex = "1.9.6"
+string-interner = "0.18.0"
 thiserror = "2.0.4"
 
 [workspace.lints.rust]

profile/Cargo.toml

@@ -0,0 +1,19 @@
+[package]
+name = "profile"
+version = "0.1.0"
+license.workspace = true
+edition.workspace = true
+authors.workspace = true
+description.workspace = true
+homepage.workspace = true
+repository.workspace = true
+rust-version.workspace = true
+publish = false
+
+[dependencies]
+omics-coordinate = { path = "../omics-coordinate" }
+
+clap = { version = "4", features = ["derive"] }
+
+[lints]
+workspace = true

profile/src/contig.rs

@@ -0,0 +1,28 @@
+//! Profiling of contigs.
+
+pub mod alloc;
+
+use clap::Parser;
+use clap::Subcommand;
+
+/// The different aspects of contigs that can be profiled.
+#[derive(Subcommand)]
+pub enum Command {
+    /// Allocations of contigs.
+    Alloc(alloc::Args),
+}
+
+/// Profiling of contigs.
+#[derive(Parser)]
+pub struct Args {
+    /// The subcommand.
+    #[command(subcommand)]
+    command: Command,
+}
+
+/// The main method.
+pub fn main(args: Args) {
+    match args.command {
+        Command::Alloc(args) => alloc::main(args),
+    }
+}

profile/src/contig/alloc.rs

@@ -0,0 +1,21 @@
+//! Profiling of contig allocations.
+
+use std::hint::black_box;
+
+use clap::Parser;
+use omics_coordinate::Contig;
+
+/// Profiling of contig allocations.
+#[derive(Parser, Debug)]
+pub struct Args {
+    /// The number of allocations to use.
+    #[arg(default_value_t = 100_000_000)]
+    n: usize,
+}
+
+/// The main method.
+pub fn main(args: Args) {
+    for _ in 0..args.n {
+        let _ = black_box(Contig::new("seq0"));
+    }
+}

profile/src/main.rs

@@ -0,0 +1,30 @@
+//! A profiling tool for developing `omics`.
+
+use clap::Parser;
+use clap::Subcommand;
+
+pub mod contig;
+
+/// The different entities that can be profiled.
+#[derive(Subcommand)]
+pub enum Command {
+    /// Contig profiling.
+    Contig(contig::Args),
+}
+
+/// Profiling of `omics` entities.
+#[derive(Parser)]
+pub struct Args {
+    /// The subcommand.
+    #[command(subcommand)]
+    command: Command,
+}
+
+/// The main method.
+pub fn main() {
+    let args = Args::parse();
+
+    match args.command {
+        Command::Contig(args) => contig::main(args),
+    }
+}