changes

Cargo.lock

@@ -37,10 +37,19 @@ dependencies = [
 ]
 
 [[package]]
-name = "bytelines"
-version = "2.2.2"
+name = "buffer-redux"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "791e4e40d13e1463dee537b254225c12c46ec7328f1817c6264873bc166f615f"
+checksum = "4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "bytecount"
+version = "0.6.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205"
 
 [[package]]
 name = "byteorder"
@@ -48,6 +57,16 @@ version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
+[[package]]
+name = "bzip2"
+version = "0.4.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8"
+dependencies = [
+ "bzip2-sys",
+ "libc",
+]
+
 [[package]]
 name = "bzip2-sys"
 version = "0.1.11+1.0.8"
@@ -135,18 +154,6 @@ dependencies = [
  "rust-htslib",
 ]
 
-[[package]]
-name = "fffx"
-version = "0.1.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f33c20b97a5cfd9d56d67e15677c1dae66c52846ee51801af32b94b70438f626"
-dependencies = [
- "bytelines",
- "flate2",
- "simdutf8",
- "static_assertions",
-]
-
 [[package]]
 name = "flate2"
 version = "1.0.28"
@@ -154,7 +161,6 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
 dependencies = [
  "crc32fast",
- "libz-sys",
  "miniz_oxide",
 ]
 
@@ -285,14 +291,12 @@ checksum = "523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149"
 
 [[package]]
 name = "minimap2"
-version = "0.1.16+minimap2.2.26"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1a6cb7c4c240401901de9c5bdfbebbcd8a43a2beb980a00c3b7c558d922ec089"
+version = "0.1.17+minimap2.2.27"
+source = "git+https://github.com/jguhlin/minimap2-rs#e09e3f252f4c34b7f327b9f256b4602a967d62b3"
 dependencies = [
- "fffx",
- "flate2",
  "libc",
  "minimap2-sys",
+ "needletail",
  "rust-htslib",
  "simdutf8",
 ]
@@ -317,6 +321,20 @@ dependencies = [
  "adler",
 ]
 
+[[package]]
+name = "needletail"
+version = "0.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d"
+dependencies = [
+ "buffer-redux",
+ "bytecount",
+ "bzip2",
+ "flate2",
+ "memchr",
+ "xz2",
+]
+
 [[package]]
 name = "newtype_derive"
 version = "0.1.6"
@@ -415,9 +433,9 @@ checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f"
 
 [[package]]
 name = "rust-htslib"
-version = "0.44.1"
+version = "0.46.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7c7eb0f29fce64a4e22578905efef3d72389058016023279a58b282eb5c0c467"
+checksum = "aec6f9ca4601beb4ae75ff8c99144dd15de5a873f6adf058da299962c760968e"
 dependencies = [
  "bio-types",
  "byteorder",
@@ -427,6 +445,7 @@ dependencies = [
  "ieee754",
  "lazy_static",
  "libc",
+ "libz-sys",
  "linear-map",
  "newtype_derive",
  "regex",
@@ -461,12 +480,6 @@ version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a"
 
-[[package]]
-name = "static_assertions"
-version = "1.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
-
 [[package]]
 name = "strum_macros"
 version = "0.25.3"
@@ -640,3 +653,12 @@ name = "windows_x86_64_msvc"
 version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8"
+
+[[package]]
+name = "xz2"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2"
+dependencies = [
+ "lzma-sys",
+]

Cargo.toml

@@ -6,7 +6,7 @@ edition = "2021"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-minimap2 = { version = "0.1.16+minimap2.2.26", features = ["htslib"]}
+minimap2 = { git = "https://github.com/jguhlin/minimap2-rs", features = ["htslib"]}
+rust-htslib = "0.46.0"
 anyhow = "1.0.75"
 log = "0.4.19"
-rust-htslib = "0.44.1"