Complete testing for num_records

Remove return value check, as it wasn't diagnostic

cyvcf2/cyvcf2.pyx

@@ -698,19 +698,29 @@ cdef class VCF(HTSFile):
             assert self.hidx == NULL
 
         if idx == NULL:
-            raise ValueError("File must be indexed to compute num_records")
+            raise ValueError(
+                "File must be indexed to compute num_records (tip: use bcftools index)")
 
         nseq = hts_idx_nseq(idx)
         total = 0;
         for tid in range(nseq):
-            ret = hts_idx_get_stat(idx, tid, &records, &v);
-            if ret < 0:
-                raise Exception("Error in `htslib::hts_idx_get_stat` ret: %d" % (ret))
+            # NOTE: the return value here doesn't seem to indicate an error
+            # condition, and correct values are computed when it returns < 0.
+            # bcftools index -n doesn't strictly check the output.
+            hts_idx_get_stat(idx, tid, &records, &v);
             total += records
         return total
 
     property num_records:
-        "Number of records in the file derived from the index"
+        """
+        The number of VCF records in the file, computed from the index.
+        If the file is not indexed (or an index has not been set using 
+        ``set_index``) a ValueError is raised.
+        
+        Note that incorrect values may be returned if a mismatched 
+        index file (i.e., the index for a different VCF file) is used.
+        This is not detected as an error condition.
+        """
         def __get__(self):
             return self._num_records()
 

cyvcf2/tests/test_reader.py

@@ -1345,6 +1345,7 @@ def test_issue17_no_gt():
     "test-strict-gt-option-flag.vcf.gz",
     "multi-contig.vcf.gz",
     "multi-contig.bcf",
+    "test.snpeff.bcf",
     ])
 def test_num_records_indexed(path):
     vcf = VCF(os.path.join(HERE, path))
@@ -1392,6 +1393,15 @@ def test_num_records_set_index_multiple_times():
         vcf.set_index(tbi_index)
         assert n == vcf.num_records
 
+def test_num_records_set_wrong_index():
+    path = os.path.join(HERE, "multi-contig.vcf.gz")
+    index = os.path.join(HERE, "test.vcf.gz.tbi")
+    vcf = VCF(path)
+    vcf.set_index(index)
+    # We compute the number of records from the index, and don't report an
+    # error
+    assert vcf.num_records == 115
+    assert vcf.num_records != len(list(vcf))
 
 @pytest.mark.parametrize("path", [
     "test-genotypes.vcf",
@@ -1400,13 +1410,3 @@ def test_num_records_no_index(path):
     vcf = VCF(os.path.join(HERE, path))
     with pytest.raises(ValueError, match="must be indexed"):
         vcf.num_records
-
-def test_num_records_incompatible_index():
-    b = VCF('{}/test.snpeff.bcf'.format(HERE))
-    with pytest.raises(Exception, match="hts_idx_get_stat"):
-        b.num_records
-    assert len(list(b)) == 10
-
-    b.set_index("{}/test-diff.csi".format(HERE))
-    print(b.num_records)
-    # Not sure why this is giving an error - is it an old file?