From b8cf8869ed842e776e1248b5398b17e1cc7be03d Mon Sep 17 00:00:00 2001
From: Vince Buffalo <vsbuffalo@gmail.com>
Date: Tue, 26 Mar 2024 13:52:16 -0700
Subject: [PATCH] Rename of `overlaps` to `overlap_widths`.

---
 Cargo.toml      |  2 +-
 src/commands.rs |  2 +-
 src/join.rs     | 10 +++++-----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index aac5ff7..10e5a47 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "granges"
-version = "0.2.2"
+version = "0.3.0"
 edition = "2021"
 license = "MIT"
 authors = ["Vince Buffalo <vsbuffalo@gmail.com>"]
diff --git a/src/commands.rs b/src/commands.rs
index 45a1ef9..ba1443c 100644
--- a/src/commands.rs
+++ b/src/commands.rs
@@ -838,7 +838,7 @@ impl FeatureDensity {
                 .left_overlaps(&gr)?
                 .map_joins(|joins| {
                     // these are merged, so this is the number of *unique* basepairs
-                    let total_overlaps: Position = joins.join.overlaps().iter().cloned().sum();
+                    let total_overlaps: Position = joins.join.overlap_widths().iter().cloned().sum();
                     total_overlaps
                 })?
             .take_data()?;
diff --git a/src/join.rs b/src/join.rs
index a40f3d2..51e8cab 100644
--- a/src/join.rs
+++ b/src/join.rs
@@ -28,7 +28,7 @@ impl GenericRange for RangeTuple {
     }
 }
 
-/// This is a special "reduced" range that stores indices
+/// This is a special "reduced" or flattened range that stores indices
 /// to multiple data elements.
 #[derive(Clone, Debug, PartialEq)]
 pub struct RangeReduced((Position, Position, HashSet<Option<usize>>));
@@ -146,16 +146,16 @@ impl LeftGroupedJoin {
 
     /// Return whether this left range has any [`LeftGroupedJoin`].
     pub fn has_overlaps(&self) -> bool {
-        !self.overlaps().is_empty()
+        !self.overlap_widths().is_empty()
     }
 
     /// Retrieve the number of right overlaps.
     pub fn num_overlaps(&self) -> usize {
-        self.overlaps().len()
+        self.overlap_widths().len()
     }
 
-    /// Retrieve the right overlaps.
-    pub fn overlaps(&self) -> Vec<Position> {
+    /// Retrieve the right overlap widths.
+    pub fn overlap_widths(&self) -> Vec<Position> {
         self.rights
             .iter()
             .map(|r| r.overlap_width(&self.left))