From 6cae26f7e099d51991b8e5b749e1c4b9f45d53a2 Mon Sep 17 00:00:00 2001
From: Shaun Jackman <sjackman@gmail.com>
Date: Mon, 15 Jul 2024 11:28:30 -0700
Subject: [PATCH] feat: Replace Arc with Rc to fix clippy lint

Fix the clippy lint:
Error: error: usage of an `Arc` that is not `Send` and `Sync`
---
 src/lib.rs          | 12 +++++-------
 star-sys/src/lib.rs |  2 --
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/src/lib.rs b/src/lib.rs
index 9917d42..e1907e5 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -7,7 +7,7 @@ use std::io::BufReader;
 use std::os::raw::c_char;
 use std::os::raw::c_int;
 use std::path::Path;
-use std::sync::Arc;
+use std::rc::Rc;
 
 use anyhow::{format_err, Error};
 use rust_htslib::bam;
@@ -16,7 +16,7 @@ use rust_htslib::bam::HeaderView;
 use star_sys::{self as bindings, Aligner as BindAligner, StarRef as BindRef};
 
 pub struct StarReference {
-    inner: Arc<InnerStarReference>,
+    inner: Rc<InnerStarReference>,
 }
 
 struct InnerStarReference {
@@ -26,8 +26,6 @@ struct InnerStarReference {
     header_view: HeaderView,
 }
 
-unsafe impl Sync for InnerStarReference {}
-
 impl Drop for InnerStarReference {
     fn drop(&mut self) {
         unsafe {
@@ -65,7 +63,7 @@ impl StarReference {
         };
 
         Ok(StarReference {
-            inner: Arc::new(inner),
+            inner: Rc::new(inner),
         })
     }
 
@@ -151,7 +149,7 @@ impl StarSettings {
 /// rust_htslib Record objects
 pub struct StarAligner {
     aligner: *mut BindAligner,
-    reference: Arc<InnerStarReference>,
+    reference: Rc<InnerStarReference>,
     sam_buf: Vec<u8>,
     aln_buf: Vec<u8>,
     fastq1: Vec<u8>,
@@ -167,7 +165,7 @@ enum AlignedRecords<'a> {
 }
 
 impl StarAligner {
-    fn new(reference: Arc<InnerStarReference>) -> StarAligner {
+    fn new(reference: Rc<InnerStarReference>) -> StarAligner {
         let aligner = unsafe { bindings::init_aligner_from_ref(reference.as_ref().reference) };
         let header_view = reference.as_ref().header_view.clone();
 
diff --git a/star-sys/src/lib.rs b/star-sys/src/lib.rs
index 2e2d2e5..1b7ba06 100644
--- a/star-sys/src/lib.rs
+++ b/star-sys/src/lib.rs
@@ -6,8 +6,6 @@ pub struct StarRef {
     _unused: [u8; 0],
 }
 
-unsafe impl Send for StarRef {}
-
 #[repr(C)]
 #[derive(Debug, Copy, Clone)]
 pub struct Aligner {