Update pyvcf submodule to accept "sites-only" VCF

CHANGELOG.rst

@@ -4,6 +4,8 @@ Changelog
 0.36.0 (in development)
 -----------------------
 
+* Update ``pyvcf`` submodule to accept "sites-only" VCF.
+
 0.35.0 (2022-07-12)
 -------------------
 

data/vcf/3.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2 
+#CHROM POS ID REF ALT QUAL FILTER INFO
+chr1 100 . A "T,C" . . .
+chr1 101 . G T . . .
+chr2 1055 . T G . . .
+chr2 3345 . A C . . .
+chr2 5594 . T G . . .

fuc/api/pyvcf.py

@@ -86,7 +86,8 @@
 do not contain the FORMAT column or sample-specific information. These are
 called "sites-only" VCF files, and normally represent genetic variation that
 has been observed in a large population. Generally, information about the
-population of origin should be included in the header.
+population of origin should be included in the header. Note that the pyvcf
+submodule supports these sites-only VCF files as well.
 
 There are several reserved keywords in the INFO and FORMAT columns that are
 standards across the community. Popular keywords are listed below:
@@ -1577,6 +1578,8 @@ class VcfFrame:
  """
  Class for storing VCF data.
 
+ Sites-only VCF files are supported.
+
  Parameters
  ----------
  meta : list
@@ -1624,7 +1627,16 @@ class VcfFrame:
 
  def _check_df(self, df):
  df = df.reset_index(drop=True)
- df = df.astype(HEADERS)
+ headers = HEADERS.copy()
+ # Handle "sites-only" VCF.
+ if 'FORMAT' not in df.columns:
+ del headers['FORMAT']
+ if set(df.columns) != set(headers):
+ raise ValueError("The input appears to be a sites-only VCF "
+ "because it's missing the FORMAT column; "
+ "however, it contains one or more incorrect "
+ f"columns: {df.columns.to_list()}.")
+ df = df.astype(headers)
  return df
 
  def __init__(self, meta, df):

test.py

@@ -51,6 +51,10 @@ def test_subset(self):
  vf = vf.subset(['Sarah', 'John'])
  self.assertEqual(len(vf.samples), 2)
 
+ def test_sites_only(self):
+ vf = pyvcf.VcfFrame.from_file(vcf_file3)
+ self.assertEqual(vf.shape, (5, 0))
+
 class TestPybed(unittest.TestCase):
 
  def test_intersect(self):