Update r-oxbow dependencies and replace deprecated APIs (#66)

* Update `r-oxbow` dependencies and replace deprecated APIs * fix(r-oxbow): repair unverified `partition_from_index_file` impl The implementation introduced in `5c329a6` attempted to return a `Vec<(u64, u16)>`, which is incompatible with `extendr` and was merged without verification. The function now correctly returns an R-compatible List with named components (`compressed_offset`, `bin_index`). --------- Co-authored-by: Trevor Manz <[email protected]>
abdenlab · Dec 1, 2024 · c94bbab · c94bbab
1 parent 0df1395
commit c94bbab
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Showing 3 changed files with 425 additions and 166 deletions.
diff --git a/oxbow/src/vpos.rs b/oxbow/src/vpos.rs
@@ -78,9 +78,9 @@ fn partition_from_index(index: &csi::Index, chunksize: u64) -> Vec<(u64, u16)> {
             continue;
         }
         let offsets = if rseq.linear_index().is_empty() {
-            get_offsets_from_binning_index(&rseq)
+            get_offsets_from_binning_index(rseq)
         } else {
-            get_offsets_from_linear_index(&rseq)
+            get_offsets_from_linear_index(rseq)
         };
         let consolidated = consolidate_chunks(&offsets, chunksize);
         partition.extend(consolidated);
@@ -114,6 +114,5 @@ fn parse_index_file(path: &str) -> io::Result<csi::Index> {
 
 pub fn partition_from_index_file(path: &str, chunksize: u64) -> Vec<(u64, u16)> {
     let index = parse_index_file(path).unwrap();
-    let partition = partition_from_index(&index, chunksize);
-    partition
+    partition_from_index(&index, chunksize)
 }