From 9899646152f13b7c0f31d31aba98bc08025dfdff Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Sun, 1 Mar 2026 22:27:31 -0700
Subject: [PATCH] Extract shared helpers for reference_name and
 next_reference_name

---
 pysam/libcalignedsegment.pxd |  3 ++
 pysam/libcalignedsegment.pyx | 57 +++++++++++++++---------------------
 2 files changed, 26 insertions(+), 34 deletions(-)

diff --git a/pysam/libcalignedsegment.pxd b/pysam/libcalignedsegment.pxd
index 1c36319f1..d823d8541 100644
--- a/pysam/libcalignedsegment.pxd
+++ b/pysam/libcalignedsegment.pxd
@@ -59,6 +59,9 @@ cdef class AlignedSegment:
     cdef object unused2
     cdef object unused3
 
+    cdef _get_reference_name(self, int tid, label)
+    cdef int _resolve_reference_id(self, reference, label) except -2
+
     # add an alignment tag with value to the AlignedSegment
     # an existing tag of the same name will be replaced.
     cpdef set_tag(self, tag, value, value_type=?, replace=?)
diff --git a/pysam/libcalignedsegment.pyx b/pysam/libcalignedsegment.pyx
index c33188cd8..953aeaa6a 100644
--- a/pysam/libcalignedsegment.pyx
+++ b/pysam/libcalignedsegment.pyx
@@ -1220,6 +1220,24 @@ cdef class AlignedSegment:
             for x from l <= x < l + l_extranul:
                 p[x] = b'\0'
 
+    cdef _get_reference_name(self, int tid, label):
+        if tid == -1:
+            return None
+        if self.header:
+            return self.header.get_reference_name(tid)
+        raise ValueError("{} unknown if no header associated with record".format(label))
+
+    cdef int _resolve_reference_id(self, reference, label) except -2:
+        if reference is None or reference == "*":
+            return -1
+        if self.header:
+            tid = self.header.get_tid(reference)
+            if tid < 0:
+                raise ValueError("reference {} does not exist in header".format(
+                    reference))
+            return tid
+        raise ValueError("{} can not be set if no header associated with record".format(label))
+
     property flag:
         """properties flag"""
         def __get__(self):
@@ -1230,24 +1248,9 @@ cdef class AlignedSegment:
     property reference_name:
         """:term:`reference` name"""
         def __get__(self):
-            if self._delegate.core.tid == -1:
-                return None
-            if self.header:
-                return self.header.get_reference_name(self._delegate.core.tid)
-            else:
-                raise ValueError("reference_name unknown if no header associated with record")
+            return self._get_reference_name(self._delegate.core.tid, "reference_name")
         def __set__(self, reference):
-            cdef int tid
-            if reference is None or reference == "*":
-                self._delegate.core.tid = -1
-            elif self.header:
-                tid = self.header.get_tid(reference)
-                if tid < 0:
-                    raise ValueError("reference {} does not exist in header".format(
-                        reference))
-                self._delegate.core.tid = tid
-            else:
-                raise ValueError("reference_name can not be set if no header associated with record")
+            self._delegate.core.tid = self._resolve_reference_id(reference, "reference_name")
 
     property reference_id:
         """:term:`reference` ID
@@ -1351,27 +1354,13 @@ cdef class AlignedSegment:
         """:term:`reference` name of the mate/next read (None if no
         AlignmentFile is associated)"""
         def __get__(self):
-            if self._delegate.core.mtid == -1:
-                return None
-            if self.header:
-                return self.header.get_reference_name(self._delegate.core.mtid)
-            else:
-                raise ValueError("next_reference_name unknown if no header associated with record")
+            return self._get_reference_name(self._delegate.core.mtid, "next_reference_name")
 
         def __set__(self, reference):
-            cdef int mtid
-            if reference is None or reference == "*":
-                self._delegate.core.mtid = -1
-            elif reference == "=":
+            if reference == "=":
                 self._delegate.core.mtid = self._delegate.core.tid
-            elif self.header:
-                mtid = self.header.get_tid(reference)
-                if mtid < 0:
-                    raise ValueError("reference {} does not exist in header".format(
-                        reference))
-                self._delegate.core.mtid = mtid
             else:
-                raise ValueError("next_reference_name can not be set if no header associated with record")
+                self._delegate.core.mtid = self._resolve_reference_id(reference, "next_reference_name")
 
     property next_reference_start:
         """the position of the mate/next read."""