Update htslib support to new MmIdx

Author: jguhlin

Cargo.toml

@@ -52,7 +52,7 @@ needletail = { version = "0.6", default-features = false}
 
 [features]
 default = ["map-file"]
-map-file = ["needletail"] #, "simdutf8"]
+map-file = ["needletail"]
 htslib = ['rust-htslib']
 simde = ["minimap2-sys/simde"]
 zlib-ng = ["minimap2-sys/zlib-ng"]

src/htslib.rs

@@ -303,9 +303,8 @@ pub struct SeqMetaData {
     pub is_alt: bool,
 }
 
-#[derive(Debug)]
 pub struct MMIndex {
-    pub inner: Arc<*mut mm_ffi::mm_idx_t>,
+    pub inner: Arc<super::MmIdx>,
 }
 
 impl MMIndex {
@@ -345,8 +344,7 @@ impl MMIndex {
 impl From<&Aligner<Built>> for MMIndex {
     fn from(aligner: &Aligner<Built>) -> Self {
         MMIndex {
-            // inner: aligner.idx.unwrap(),
-            inner: std::sync::Arc::clone(&aligner.idx.as_ref().unwrap()),
+            inner: std::sync::Arc::clone(aligner.idx.as_ref().unwrap()),
         }
     }
 }