From 9c2c06655986bb6ac8b5c3e043b683df5b02e41f Mon Sep 17 00:00:00 2001
From: Seung-been Lee <sbstevenlee@gmail.com>
Date: Thu, 6 Jun 2024 20:18:12 +0900
Subject: [PATCH] Update `pyvcf.has_chr_prefix`:

* Update :meth:`pyvcf.has_chr_prefix` method to ignore the HLA contigs for GRCh38.
---
 CHANGELOG.rst    | 2 ++
 fuc/api/pyvcf.py | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index cde6191..360488c 100644
--- 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
index 8211b5b..bb714f7 100644
--- 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: