Use memoryviews to optimize array_to_qualitystring (PR #1363)

The data is contiguous so we can use [::1] to omit stride calculations.
Using explicit memoryviews rather than the previous array indexing code 
leads to a 100x speedup within this function.

Author: jchorl

pysam/libcutils.pyx

@@ -46,14 +46,19 @@ cpdef array_to_qualitystring(c_array.array qualities, int offset=33):
     """convert an array of quality values to a string."""
     if qualities is None:
         return None
-    cdef int x
 
-    cdef c_array.array result
-    result = c_array.clone(qualities, len(qualities), zero=False)
+    cdef const unsigned char[::1] qualities_view = qualities
+    cdef size_t n = qualities_view.shape[0]
 
-    for x from 0 <= x < len(qualities):
-        result[x] = qualities[x] + offset
-    return force_str(result.tobytes())
+    cdef bytearray result_ba = bytearray(n)
+    cdef unsigned char[::1] result_view = result_ba
+
+    cdef size_t i
+
+    for i in range(n):
+        result_view[i] = qualities_view[i] + offset
+
+    return force_str(bytes(result_ba))
 
 
 cpdef qualities_to_qualitystring(qualities, int offset=33):

tests/AlignedSegment_test.py

@@ -1901,5 +1901,27 @@ def test_string_export_import_with_tags(self):
         self.assertEqual(a, b)
 
 
+class TestArrayUtilities(unittest.TestCase):
+    def test_array_to_qualstr(self):
+        data = [
+            "",
+            "Q",
+            """!"#$%&'()*+,-./012...xyz{|}~""",
+            ">>?AB",
+            "ABDDEFGHIJabcdefghij",
+            "ACAFFGGFFFJDFJHHJIJIHKGGHKHHIJHHHJ7123" * 50,
+        ]
+
+        for qual in data:
+            qual_array = pysam.qualitystring_to_array(qual)
+            result = pysam.array_to_qualitystring(qual_array)
+            self.assertEqual(result, qual)
+
+    def test_longarray_to_qualstr(self):
+        qual_array = array.array('l', [64, 65, 66, 67, 68])
+        with self.assertRaises(ValueError):
+            pysam.array_to_qualitystring(qual_array)
+
+
 if __name__ == "__main__":
     unittest.main()

tests/libcutils_bench.py

@@ -0,0 +1,10 @@
+"""Benchmarking the libcutils module. Usage::
+
+pytest tests/libcutils_bench.py
+"""
+import pysam
+
+
+def test_array_to_qualitystring_long_sequences(benchmark):
+    result = benchmark(pysam.array_to_qualitystring, pysam.qualitystring_to_array("123") * 500)
+    assert result == "123" * 500