chore: generate C bindings for minimap crate only into output dir

In `minimap-sys` crate: this removes hardcoded `bindings.rs` in favor of always dynamically rebuilding them with `rust-bindgen`. The `vendored` feature of `minimap-sys` is removed and is always enabled now.

This is required to avoid clashes when compiling for different platforms and operating systems - the bindings are generated slightly differently on different setups.

It's a [best practice](https://rust-lang.github.io/rust-bindgen/tutorial-3.html) anyways.

Cargo.toml

@@ -35,15 +35,13 @@ zstd = { version = "=0.13.2", features = ["zstdmt"] }
 
 
 minimap2 = { path = "packages/minimap2", features = ["serde"] }
-minimap2-sys = { path = "packages/minimap2-sys", features = ["simde", "static", "vendored", "stock-zlib"] }
-#minimap2-sys = { path = "packages/minimap2-sys", features = ["simde", "vendored"] }
+minimap2-sys = { path = "packages/minimap2-sys", features = ["simde", "static", "stock-zlib"] }
 
 
 approx = "=0.5.1"
 atty = "=0.2.14"
 auto_ops = "=0.3.0"
 bio = "=2.0.3"
-bio-types = "=1.0.4"
 chrono = { version = "=0.4.38", default-features = false, features = ["clock", "std", "wasmbind"] }
 clap = { version = "=4.5.17", features = ["derive", "color", "unicode", "unstable-styles"] }
 clap-markdown = "=0.1.4"
@@ -63,26 +61,21 @@ itertools = "=0.13.0"
 lazy_static = "=1.5.0"
 log = "=0.4.22"
 maplit = "=1.0.2"
-memoize = { version = "=0.4.2", features = ["full"] }
 ndarray = { version = "=0.16.1", features = ["rayon", "serde", "blas", "approx"] }
-ndarray-rand = "=0.15.0"
 ndarray-stats = "=0.6.0"
 noodles = { version = "=0.60.0", features = ["core", "sam"] }
 num = "=0.4.3"
-num-integer = "=0.1.46"
 num-traits = "=0.2.19"
 num_cpus = "=1.16.0"
 ordered-float = { version = "=4.2.2", features = ["serde"] }
 parking_lot = { version = "=0.12.3", features = ["deadlock_detection", "hardware-lock-elision", "serde", "arc_lock"] }
 pretty_assertions = "=1.4.1"
 pretty_dtoa = "=0.3.0"
 rand = { version = "=0.8.5", features = ["serde1", "log"] }
-rand_distr = { version = "=0.4.3", features = ["serde1", "std_math"] }
 rand_isaac = { version = "=0.3.0", features = ["serde1"] }
 rayon = "=1.10.0"
 regex = "=1.11.0"
 rstest = "=0.22.0"
-rstest_reuse = "=0.7.0"
 schemars = { version = "=1.0.0-alpha.15", features = ["chrono04", "either1", "enumset1", "indexmap2", "raw_value", "schemars_derive", "preserve_order"] }
 serde = { version = "=1.0.210", features = ["derive"] }
 serde-aux = "=4.5.0"

packages/minimap2-sys/Cargo.toml

@@ -33,12 +33,11 @@ exclude = [
 libz-sys = { version = "1.1.20", default-features = false }
 
 [build-dependencies]
-bindgen = { version = "0.70.1", features = ["which-rustfmt", "runtime"], optional = true }
+bindgen = { version = "0.70.1", features = ["which-rustfmt", "runtime"] }
 cc = { version = "1.1.21" }
 
 [features]
 default = ["libz-sys/libc"]
-vendored = ["bindgen"]
 sse2only = []
 simde = []
 noopt = []

packages/minimap2-sys/build.rs

@@ -209,7 +209,6 @@ fn sse2only(cc: &mut cc::Build) {
   }
 }
 
-#[cfg(feature = "bindgen")]
 fn gen_bindings() {
   let out_path = PathBuf::from(env::var_os("OUT_DIR").unwrap());
 
@@ -226,15 +225,8 @@ fn gen_bindings() {
   bigings
     .write_to_file(out_path.join("bindings.rs"))
     .expect("Unable to create bindings");
-
-  bigings
-    .write_to_file("src/bindings.rs")
-    .expect("Unable to create bindings");
 }
 
-#[cfg(not(feature = "bindgen"))]
-fn gen_bindings() {}
-
 fn main() {
   compile();
   gen_bindings();