From 92c8bcecf02f40d18d5122e68a2650ec23e683e7 Mon Sep 17 00:00:00 2001
From: mholt <mholt@pacificbiosciences.com>
Date: Tue, 21 May 2024 05:54:05 -0700
Subject: [PATCH] resets l_extranul before trying to set it

---
 src/bam/record_serde.rs | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/bam/record_serde.rs b/src/bam/record_serde.rs
index 651867030..1bf8a2fa1 100644
--- a/src/bam/record_serde.rs
+++ b/src/bam/record_serde.rs
@@ -8,6 +8,8 @@ use serde_bytes::{ByteBuf, Bytes};
 use crate::bam::record::Record;
 
 fn fix_l_extranul(rec: &mut Record) {
+    // first, reset the number of extranuls to 0 for calling .qname(); then calculate how many we actually have
+    rec.inner_mut().core.l_extranul = 0;
     let l_extranul = rec.qname().iter().rev().take_while(|x| **x == 0u8).count() as u8;
     rec.inner_mut().core.l_extranul = l_extranul;
 }