From d19452ee7537d84b460020be1142bd4ef979f55c Mon Sep 17 00:00:00 2001
From: "J. Christian Heide" <christian_heide@eva.mpg.de>
Date: Thu, 17 Aug 2023 11:07:24 +0200
Subject: [PATCH] Use Cargo's dependency patching feature for `bio`

---
 Cargo.lock | 11 +++++++++--
 Cargo.toml |  5 ++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 1908f02..01aefa4 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -110,8 +110,8 @@ dependencies = [
 
 [[package]]
 name = "bio"
-version = "0.42.0-mapAD"
-source = "git+https://github.com/jch-13/rust-bio.git?branch=occ_small_k#12ccdd1cffc95034fe4348d64469a3477606aa09"
+version = "1.3.1"
+source = "git+https://github.com/jch-13/rust-bio.git?branch=occ_small_k#3a6d2377842ae975349f3edc8062e8a9ee362438"
 dependencies = [
  "anyhow",
  "approx",
@@ -121,6 +121,7 @@ dependencies = [
  "bytecount",
  "csv",
  "custom_derive",
+ "editdistancek",
  "enum-map",
  "fxhash",
  "getset",
@@ -524,6 +525,12 @@ dependencies = [
  "crypto-common",
 ]
 
+[[package]]
+name = "editdistancek"
+version = "1.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3e02df23d5b1c6f9e69fa603b890378123b93073df998a21e6e33b9db0a32613"
+
 [[package]]
 name = "either"
 version = "1.9.0"
diff --git a/Cargo.toml b/Cargo.toml
index f11ee72..faf51b6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -13,7 +13,7 @@ clap = { version = "4.0", features = ["cargo", "string"] }
 log = "0.4"
 simple_logger = "4.0"
 bincode = "1.3"
-bio = { git = "https://github.com/jch-13/rust-bio.git", branch = "occ_small_k", features = ["runtime-dispatch-simd"] }
+bio = { version = "1.3", features = ["runtime-dispatch-simd"] }
 assert_approx_eq = "1.1"
 smallvec = "1.8"
 rand = "0.8"
@@ -30,6 +30,9 @@ noodles = { version = "0.47", features = ["bam", "bgzf", "core", "cram", "fasta"
 time = { version = "0.3", features = ["local-offset"] }
 flate2 = "1.0"
 
+[patch.crates-io]
+bio = { git = "https://github.com/jch-13/rust-bio.git", branch = "occ_small_k" }
+
 [dev-dependencies]
 criterion = "0.5"
 tempfile = "3.3"