From 353d850dd1934e73465f363a6ead4fb393169d2d Mon Sep 17 00:00:00 2001 From: Madhava Jay Date: Wed, 27 May 2026 22:18:12 +1000 Subject: [PATCH] Patch htslib-rs/noodles git deps to rv-managed local paths bcftools-rs and samtools-rs (and htslib-rs itself) now declare htslib-rs and noodles as git deps. Cargo identifies them by URL, so this workspace can [patch] both URLs to the single rv-managed local checkout under vendor/rust/, collapsing what cargo would otherwise see as three independent path sources into one lockfile entry. Also set net.git-fetch-with-cli so cargo uses the system git for the upstream verification fetch (respects ssh config and credentials). --- .cargo/config.toml | 2 ++ rust/Cargo.toml | 6 ++++++ 2 files changed, 8 insertions(+) create mode 100644 .cargo/config.toml diff --git a/.cargo/config.toml b/.cargo/config.toml new file mode 100644 index 0000000..c91c3f3 --- /dev/null +++ b/.cargo/config.toml @@ -0,0 +1,2 @@ +[net] +git-fetch-with-cli = true diff --git a/rust/Cargo.toml b/rust/Cargo.toml index 0b9ea37..b521b68 100644 --- a/rust/Cargo.toml +++ b/rust/Cargo.toml @@ -38,3 +38,9 @@ noodles-refget = { path = "../noodles/noodles-refget" } noodles-sam = { path = "../noodles/noodles-sam" } noodles-tabix = { path = "../noodles/noodles-tabix" } noodles-vcf = { path = "../noodles/noodles-vcf" } + +[patch."https://github.com/madhavajay/htslib-rs.git"] +htslib-rs = { path = "../vendor/rust/htslib-rs/crates/htslib-rs" } + +[patch."https://github.com/madhavajay/noodles.git"] +noodles = { path = "../noodles/noodles" }