From c9b8086dd83a23774f659d87997e648d81f0159b Mon Sep 17 00:00:00 2001
From: Andy Pohl <andyp@exai.bio>
Date: Sun, 3 Mar 2024 13:57:48 -0600
Subject: [PATCH] hack ref_len -1

---
 d4-hts/src/alignment/alignment_ext.rs | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/d4-hts/src/alignment/alignment_ext.rs b/d4-hts/src/alignment/alignment_ext.rs
index 53de668..f70220d 100644
--- a/d4-hts/src/alignment/alignment_ext.rs
+++ b/d4-hts/src/alignment/alignment_ext.rs
@@ -17,7 +17,7 @@ impl<'a> Alignment<'a> {
     }
 
     pub fn ref_len(&self) -> usize {
-        self.cigar()
+        let length: usize = self.cigar()
             .filter_map(|x| {
                 if x.in_reference() {
                     Some(x.len as usize)
@@ -25,7 +25,8 @@ impl<'a> Alignment<'a> {
                     None
                 }
             })
-            .sum()
+            .sum();
+        length - 1
     }
 
     pub fn ref_end(&self) -> usize {