Update pyvcf.has_chr_prefix:

* Update :meth:`pyvcf.has_chr_prefix` method to ignore the HLA contigs for GRCh38.
sbslee · Jun 6, 2024 · 9c2c066 · 9c2c066
1 parent 541c186
commit 9c2c066
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,8 @@ Changelog
 0.38.0 (in development)
 -----------------------
 
+* Update :meth:`pyvcf.has_chr_prefix` method to ignore the HLA contigs for GRCh38.
+
 0.37.0 (2023-09-09)
 -------------------
 

diff --git a/fuc/api/pyvcf.py b/fuc/api/pyvcf.py
@@ -763,6 +763,8 @@ def has_chr_prefix(file, size=1000):
  Return True if all of the sampled contigs from a VCF file have the
  (annoying) 'chr' string.
 
+ For GRCh38, the HLA contigs will be ignored.
+
  Parameters
  ----------
  file : str
@@ -779,6 +781,8 @@ def has_chr_prefix(file, size=1000):
  vcf = VariantFile(file)
  for record in vcf.fetch():
  n += 1
+ if record.chrom.startswith('HLA'):
+ continue
  if 'chr' not in record.chrom:
  return False
  if n > size: