Handle MD:Z and MD:A types in build_alignment_sequence()

Check the type code and raise TypeError instead of segfaulting if it is
not a Z string. Also accept MD:A to work around HTSeq bug that writes
1-character strings as MD:A:v. Fixes #1226. Add tests.

pysam/libcalignedsegment.pyx

@@ -757,7 +757,18 @@ cdef inline bytes build_alignment_sequence(bam1_t * src):
         elif op == BAM_CHARD_CLIP:
             pass # advances neither
 
-    cdef char * md_tag = <char*>bam_aux2Z(md_tag_ptr)
+    cdef char *md_tag, md_buffer[2];
+    cdef uint8_t md_typecode = md_tag_ptr[0]
+    if md_typecode == b'Z':
+        md_tag = bam_aux2Z(md_tag_ptr)
+    elif md_typecode == b'A':
+        # Work around HTSeq bug that writes 1-character strings as MD:A:v
+        md_buffer[0] = bam_aux2A(md_tag_ptr)
+        md_buffer[1] = b'\0'
+        md_tag = md_buffer
+    else:
+        raise TypeError('Tagged field MD:{}:<value> does not have expected type MD:Z'.format(chr(md_typecode)))
+
     cdef int md_idx = 0
     cdef char c
     s_idx = 0

tests/AlignedSegment_test.py

@@ -776,6 +776,32 @@ def test_get_aligned_pairs_uppercase_md(self):
             ],
         )
 
+    def test_get_aligned_pairs_1character_md(self):
+        a = self.build_read()
+        a.query_sequence = "A" * 7
+        a.cigarstring = "7M"
+        a.set_tag("MD", "7", value_type="A")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "A"),
+                (5, 25, "A"),
+                (6, 26, "A"),
+            ],
+        )
+
+    def test_get_aligned_pairs_bad_type_md(self):
+        a = self.build_read()
+        a.query_sequence = "A" * 7
+        a.cigarstring = "7M"
+        a.set_tag("MD", 7)
+        with self.assertRaises(TypeError):
+            a.get_aligned_pairs(with_seq=True)
+
     def testNoSequence(self):
         """issue 176: retrieving length without query sequence
         with soft-clipping.