diff --git a/src/main.rs b/src/main.rs
index 937b44f..ea760fc 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -126,6 +126,7 @@ fn fcount(
     let mut line_str = String::new();
     let mut startpos: u32;
     let mut endpos: u32;
+    let mut check_end: bool;
 
     loop {
         match reader.read_line(&mut line_str) {
@@ -156,6 +157,7 @@ fn fcount(
         // check if cell is to be included
         let cell_barcode: &str = fields[3];
         if let Some(&cell_index) = cells.get(cell_barcode) {
+            check_end = true;
 
             // create intervals from fragment entry
             let seqname: &str = fields[0];
@@ -165,15 +167,23 @@ fn fcount(
                 startpos = fields[1].parse().map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;
                 endpos = fields[2].parse().map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;
     
-                // find overlapping peaks
                 if let Some(olap_start) = find_overlaps(&peaks, seqname, startpos, startpos+1) {
+
                     for peak_index in olap_start {
                         *peak_cell_counts[peak_index.0].entry(cell_index).or_insert(0) += 1;
+
+                        // check if fragment end is behind peak end (if so, it overlaps and we don't need a full search)
+                        if endpos < peak_index.1 {
+                            check_end = false;
+                            *peak_cell_counts[peak_index.0].entry(cell_index).or_insert(0) += 1;
+                        }
                     }
                 }
-                if let Some(olap_end) = find_overlaps(&peaks, seqname, endpos, endpos+1) {
-                    for peak_index in olap_end {
-                        *peak_cell_counts[peak_index.0].entry(cell_index).or_insert(0) += 1;
+                if check_end {
+                    if let Some(olap_end) = find_overlaps(&peaks, seqname, endpos, endpos+1) {
+                        for peak_index in olap_end {
+                            *peak_cell_counts[peak_index.0].entry(cell_index).or_insert(0) += 1;
+                        }
                     }
                 }
             }