Improve cigarstring performance

pysam/libcalignedsegment.pyx

@@ -75,6 +75,7 @@ from pysam.libcutils cimport force_bytes, force_str, \
     charptr_to_str, charptr_to_bytes
 from pysam.libcutils cimport qualities_to_qualitystring, qualitystring_to_array, \
     array_to_qualitystring
+from libc.stdio cimport snprintf
 
 # Constants for binary tag conversion
 cdef char * htslib_types = 'cCsSiIf'
@@ -1279,13 +1280,41 @@ cdef class AlignedSegment:
         empty string.
         '''
         def __get__(self):
-            c = self.cigartuples
-            if c is None:
+            cdef uint32_t *cigar_p
+            cdef bam1_t *src
+            cdef uint32_t op, l
+            cdef int k
+            cdef int ret
+            cdef int pos = 0
+            cdef int size = 16
+            cdef char buf[16]
+            cdef char *s = buf
+
+            src = self._delegate
+            if pysam_get_n_cigar(src) == 0:
                 return None
-            # reverse order
-            else:
-                return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c])
 
+            cigar_p = pysam_bam_get_cigar(src)
+            while True:
+                for k from 0 <= k < pysam_get_n_cigar(src):
+                    op = cigar_p[k] & BAM_CIGAR_MASK
+                    l = cigar_p[k] >> BAM_CIGAR_SHIFT
+                    ret = snprintf(s + pos, size - pos, "%u%c", l, CODE2CIGAR[op])
+                    if ret >= size - pos:
+                        pos = 0
+                        size = size * 2
+                        if s != buf:
+                            free(s)
+                        s = <char *>malloc(size)
+                        break
+                    pos += ret
+                else:
+                    break
+            try:
+                return s[:pos].decode("utf8")
+            finally:
+                if s != buf:
+                    free(s)
         def __set__(self, cigar):
             if cigar is None or len(cigar) == 0:
                 self.cigartuples = []

tests/AlignedSegment_test.py

@@ -1028,6 +1028,16 @@ def testStats(self):
             expected[1][i] = 1
             self.assertEqual([list(x) for x in a.get_cigar_stats()], expected)
 
+        for i in range(1, 100):
+            cigarstring = "".join("10{}".format(x)
+                                  for x in iter("MIDNSHP=X")) * i
+            a.cigarstring = cigarstring
+            self.assertEqual(a.cigarstring, cigarstring)
+            expected = [[i * 10 for j in range(len("MIDNSHP=X"))] + [0, 0],
+                        [i for j in range(len("MIDNSHP=X"))] + [0, 0]]
+            obtained = [list(x) for x in a.get_cigar_stats()]
+            self.assertEqual(obtained, expected)
+
         a.cigarstring = "10M"
         a.set_tag("NM", 5)
         self.assertEqual(