From 22ae6085d82531a6102d1c46e865ba92b96f0dc2 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 1 Jan 2025 15:39:02 -0600
Subject: [PATCH 1/3] align SortedRanges to cache line boundary for improved
 memory access

---
 Cargo.lock  | 4 ++--
 src/impg.rs | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 40cac35..7c4313d 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -434,9 +434,9 @@ checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
 [[package]]
 name = "syn"
-version = "2.0.93"
+version = "2.0.94"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c786062daee0d6db1132800e623df74274a0a87322d8e183338e01b3d98d058"
+checksum = "987bc0be1cdea8b10216bd06e2ca407d40b9543468fafd3ddfb02f36e77f71f3"
 dependencies = [
  "proc-macro2",
  "quote",
diff --git a/src/impg.rs b/src/impg.rs
index 0a0ea28..89340b4 100644
--- a/src/impg.rs
+++ b/src/impg.rs
@@ -112,6 +112,8 @@ pub struct SerializableInterval {
     metadata: QueryMetadata,
 }
 
+// Align ranges to cache line boundary for better memory access
+#[repr(align(64))]
 #[derive(Debug, Default, Clone)]
 pub struct SortedRanges {
     pub ranges: Vec<(i32, i32)>

From 6c5a3b85c3d1d2e2c5718d35396cb64d703f246f Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 1 Jan 2025 20:27:01 -0600
Subject: [PATCH 2/3] keep the stack sorted and merged by key

---
 src/impg.rs | 34 +++++++++++++++++++++++-----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/src/impg.rs b/src/impg.rs
index 89340b4..a318b3d 100644
--- a/src/impg.rs
+++ b/src/impg.rs
@@ -112,8 +112,6 @@ pub struct SerializableInterval {
     metadata: QueryMetadata,
 }
 
-// Align ranges to cache line boundary for better memory access
-#[repr(align(64))]
 #[derive(Debug, Default, Clone)]
 pub struct SortedRanges {
     pub ranges: Vec<(i32, i32)>
@@ -142,22 +140,22 @@ impl SortedRanges {
         } else {
             (new_range.1, new_range.0)
         };
-
+    
         // Return regions that don't overlap with existing ranges
         let mut non_overlapping = Vec::new();
         let mut current = start;
-
+    
         // Find the first range that could overlap
         let mut i = match self.ranges.binary_search_by_key(&start, |&(s, _)| s) {
             Ok(pos) => pos,
             Err(pos) => pos,
         };
-
+    
         // Check previous range for overlap
         if i > 0 && self.ranges[i - 1].1 > start {
             i -= 1;
         }
-
+    
         // Process all potentially overlapping ranges
         while i < self.ranges.len() && current < end {
             let (range_start, range_end) = self.ranges[i];
@@ -170,11 +168,11 @@ impl SortedRanges {
             current = max(current, range_end);
             i += 1;
         }
-
+    
         if current < end {
             non_overlapping.push((current, end));
         }
-
+    
         // Now insert the range while maintaining sorted order and merging overlaps
         match self.ranges.binary_search_by_key(&start, |&(s, _)| s) {
             Ok(pos) | Err(pos) => {
@@ -186,12 +184,12 @@ impl SortedRanges {
                     self.ranges[pos].0 = min(start, self.ranges[pos].0);
                     self.ranges[pos].1 = max(end, self.ranges[pos].1);
                     self.merge_forward_from(pos);
-                } else {
+        } else {
                     self.ranges.insert(pos, (start, end));
                 }
             }
         }
-
+    
         non_overlapping
     }
 
@@ -432,7 +430,21 @@ impl Impg {
                         }
                     }
                 });
-            }
+
+                // Merge contiguous/overlapping ranges with same sequence_id
+                stack.sort_by_key(|(id, start, _)| (*id, *start));
+                let mut write = 0;
+                for read in 1..stack.len() {
+                    if stack[write].0 == stack[read].0 &&   // Same sequence_id 
+                        stack[write].2 >= stack[read].1 {   // Overlapping or contiguous
+                        stack[write].2 = stack[write].2.max(stack[read].2);
+                    } else {
+                        write += 1;
+                        stack.swap(write, read);
+                    }
+                }
+                stack.truncate(write + 1);
+            }            
         }
 
         results

From b14d1e2f33ec6770f4fe761dac3abdfa2a9fc3c9 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Thu, 2 Jan 2025 18:41:20 -0600
Subject: [PATCH 3/3] performance tweak

---
 src/impg.rs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/impg.rs b/src/impg.rs
index a318b3d..ec5770f 100644
--- a/src/impg.rs
+++ b/src/impg.rs
@@ -384,14 +384,14 @@ impl Impg {
             .map(|(&k, v)| (k, (*v).clone()))
             .collect()
         } else {
-            FxHashMap::default()
+            FxHashMap::with_capacity_and_hasher(self.seq_index.len(), Default::default())
         };
         // Initialize first visited range for target_id if not already present
         visited_ranges.entry(target_id)
             .or_default()
             .insert((range_start, range_end));
 
-        while let Some((current_target_id, current_target_start, current_target_end)) = stack.pop() {
+                while let Some((current_target_id, current_target_start, current_target_end)) = stack.pop() {
             if let Some(tree) = self.trees.get(&current_target_id) {
                 tree.query(current_target_start, current_target_end, |interval| {
                     let metadata = &interval.metadata;