feat: added strandedness to closest and match bedrs-2.0 api for call

src/cli/closest.rs

@@ -1,7 +1,6 @@
+use super::{outputs::Output, overlap_predicates::WrapStrandedness, DualInput};
 use clap::Parser;
 
-use super::{outputs::Output, DualInput};
-
 /// Finds the closest interval in a secondary BED file for all intervals in a primary BED file
 #[derive(Parser, Debug)]
 #[clap(next_help_heading = "Global options")]
@@ -27,7 +26,11 @@ pub struct ClosestParams {
     #[clap(short = 'd', long, conflicts_with = "upstream")]
     pub downstream: bool,
 
+    /// Strand-specificity of closest intervals
+    #[clap(short, long, default_value = "i")]
+    pub strandedness: WrapStrandedness,
+
     /// Specify that the input files are already presorted
-    #[clap(short, long)]
+    #[clap(short = 'S', long)]
     pub sorted: bool,
 }

src/commands/closest.rs

@@ -51,13 +51,14 @@ where
     Renamer: Rename<'a, Ia, Na> + Rename<'a, Ib, Nb>,
 {
     sort_pairs(&mut a_set, &mut b_set, params.sorted);
+    let method = params.strandedness.into();
     let pairs_iter = a_set
         .iter()
         .map(|query| {
             let target = match params.into() {
-                ClosestType::Both => b_set.closest(query),
-                ClosestType::Upstream => b_set.closest_upstream(query),
-                ClosestType::Downstream => b_set.closest_downstream(query),
+                ClosestType::Both => b_set.closest(query, method),
+                ClosestType::Upstream => b_set.closest_upstream(query, method),
+                ClosestType::Downstream => b_set.closest_downstream(query, method),
             }
             .expect("Could not build closest index");
             (query, target)