From 1c2a397fd63e850f023e800b43208b8184748ab7 Mon Sep 17 00:00:00 2001
From: Archie Young <750826700@qq.com>
Date: Fri, 10 Apr 2026 17:40:41 +0800
Subject: [PATCH] emit base qualities for unaligned sequences

---
 src/alignment_io.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/alignment_io.cpp b/src/alignment_io.cpp
index d4dd3da..4436d36 100644
--- a/src/alignment_io.cpp
+++ b/src/alignment_io.cpp
@@ -913,6 +913,12 @@ gafkluge::GafRecord alignment_to_gaf(function<size_t(nid_t)> node_to_length,
             string cs_cigar_str = "+" + aln.sequence();
             gaf.opt_fields["cs"] = make_pair("Z", std::move(cs_cigar_str));
         }
+
+        // emit base qualities for unaligned sequences
+        // optional base qualities                                                                                                                      
+        if (base_quals && !aln.quality().empty()) {                                                                                                     
+            gaf.opt_fields["bq"] = make_pair("Z", string_quality_short_to_char(aln.quality()));                                                         
+        }
     }
 
     // optional frag_next/prev names