From a970aafa3d0817caf0be3f05198f923beadc6605 Mon Sep 17 00:00:00 2001
From: Joseph Guhlin <joseph.guhlin@gmail.com>
Date: Wed, 13 Mar 2024 08:17:46 +1300
Subject: [PATCH 1/4] Update to minimap v2.27

---
 minimap2-sys/Cargo.lock | 31 +++++++++++++++++--------------
 minimap2-sys/minimap2   |  2 +-
 2 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/minimap2-sys/Cargo.lock b/minimap2-sys/Cargo.lock
index 2a97790..c33c54b 100644
--- a/minimap2-sys/Cargo.lock
+++ b/minimap2-sys/Cargo.lock
@@ -13,16 +13,16 @@ dependencies = [
 
 [[package]]
 name = "bindgen"
-version = "0.66.1"
+version = "0.69.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f2b84e06fc203107bfbad243f4aba2af864eb7db3b1cf46ea0a023b0b433d2a7"
+checksum = "a00dc851838a2120612785d195287475a3ac45514741da670b735818822129a0"
 dependencies = [
  "bitflags",
  "cexpr",
  "clang-sys",
+ "itertools",
  "lazy_static",
  "lazycell",
- "peeking_take_while",
  "proc-macro2",
  "quote",
  "regex",
@@ -40,9 +40,9 @@ checksum = "630be753d4e58660abd17930c71b647fe46c27ea6b63cc59e1e3851406972e42"
 
 [[package]]
 name = "cc"
-version = "1.0.79"
+version = "1.0.90"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f"
+checksum = "8cd6604a82acf3039f1144f54b8eb34e91ffba622051189e71b781822d5ee1f5"
 
 [[package]]
 name = "cexpr"
@@ -91,6 +91,15 @@ version = "0.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
 
+[[package]]
+name = "itertools"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569"
+dependencies = [
+ "either",
+]
+
 [[package]]
 name = "lazy_static"
 version = "1.4.0"
@@ -121,9 +130,9 @@ dependencies = [
 
 [[package]]
 name = "libz-sys"
-version = "1.1.11"
+version = "1.1.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "121f7402cc6ab5821dad08d1b9d11618a9ea4da992343909fecf8e430e86364c"
+checksum = "037731f5d3aaa87a5675e895b63ddff1a87624bc29f77004ea829809654e48f6"
 dependencies = [
  "cc",
  "cmake",
@@ -146,7 +155,7 @@ checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
 
 [[package]]
 name = "minimap2-sys"
-version = "0.1.14+minimap2.2.26"
+version = "0.1.16+minimap2.2.26"
 dependencies = [
  "bindgen",
  "cc",
@@ -170,12 +179,6 @@ version = "1.18.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d"
 
-[[package]]
-name = "peeking_take_while"
-version = "0.1.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "19b17cddbe7ec3f8bc800887bab5e717348c95ea2ca0b1bf0837fb964dc67099"
-
 [[package]]
 name = "pkg-config"
 version = "0.3.27"
diff --git a/minimap2-sys/minimap2 b/minimap2-sys/minimap2
index e28a55b..b676250 160000
--- a/minimap2-sys/minimap2
+++ b/minimap2-sys/minimap2
@@ -1 +1 @@
-Subproject commit e28a55be86b298708a2a67c924d665a00b8d829c
+Subproject commit b6762503a9c9af34ae02f56784035ff852ed04a5

From 96236ccdcec22e0ce1bcb3d21185e34859f05732 Mon Sep 17 00:00:00 2001
From: Joseph Guhlin <joseph.guhlin@gmail.com>
Date: Wed, 13 Mar 2024 08:28:04 +1300
Subject: [PATCH 2/4] Update to minimap v2.27

---
 Cargo.toml | 2 +-
 README.md  | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/Cargo.toml b/Cargo.toml
index 54828bc..c8ec166 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "minimap2"
-version = "0.1.16+minimap2.2.26"
+version = "0.1.17+minimap2.2.27"
 edition = "2021"
 authors = ["Joseph Guhlin <joseph.guhlin@gmail.com>"]
 license = "MIT OR Apache-2.0"
diff --git a/README.md b/README.md
index a2e9f42..3077298 100644
--- a/README.md
+++ b/README.md
@@ -157,6 +157,11 @@ and/or:
 > *Bioinformatics*, **37**:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
 
 # Changelog
+### 0.1.17 minimap2 2.27
+* Mark bam::Record objects as supplementary. #52  @PB-DB
+* Only use rust-htslib/curl when curl feature is enabled. #53 @PB-DB
+* Update to minimap2 v2.27 @jguhlin
+
 ### 0.1.16 minimap2 2.26
 * Much better cross compilation support thanks to @Adoni5
 

From a3917bbd14f15264d9ce767198154a1a61e2cd70 Mon Sep 17 00:00:00 2001
From: Joseph Guhlin <joseph.guhlin@gmail.com>
Date: Wed, 13 Mar 2024 08:30:51 +1300
Subject: [PATCH 3/4] .

---
 src/lib.rs | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/lib.rs b/src/lib.rs
index c771599..d3a12a6 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -1216,7 +1216,6 @@ pub fn detect_compression_format(buffer: &[u8]) -> Result<CompressionType, &'sta
 #[cfg(test)]
 mod tests {
     use super::*;
-    use std::mem::MaybeUninit;
 
     #[test]
     fn compression_format_detections() {
@@ -1285,10 +1284,8 @@ mod tests {
     #[test]
     fn mapopt() {
         let _x: mm_mapopt_t = Default::default();
-        drop(_x);
         println!("One done...");
         let _x: MapOpt = Default::default();
-        drop(_x);
         println!("Second...");
     }
 

From 46575fa43dc553af94e4f8d5302b6088b3fb8192 Mon Sep 17 00:00:00 2001
From: Joseph Guhlin <joseph.guhlin@gmail.com>
Date: Wed, 13 Mar 2024 08:32:17 +1300
Subject: [PATCH 4/4] .

---
 minimap2-sys/mm2-fast | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/minimap2-sys/mm2-fast b/minimap2-sys/mm2-fast
index 10bde16..88d096b 160000
--- a/minimap2-sys/mm2-fast
+++ b/minimap2-sys/mm2-fast
@@ -1 +1 @@
-Subproject commit 10bde16019f958572c4416e7cad1f5e17ed8592a
+Subproject commit 88d096b1c5dd053693706f46121554fe75e4de4a