From e62c91640de07d218a63f6abd9d3d9051d056b6c Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Mon, 25 Nov 2019 15:48:14 +0100
Subject: [PATCH] Use get_header_type to determine if RGQ is present
---
vtools/evaluate.py | 18 ++++++------------
1 file changed, 6 insertions(+), 12 deletions(-)
diff --git a/vtools/evaluate.py b/vtools/evaluate.py
index 91e18ee..396d689 100644
--- a/vtools/evaluate.py
+++ b/vtools/evaluate.py
@@ -48,19 +48,13 @@ def parse_variants(ref: str, call: List[str], pos: List[str],
def RGQ_header_defined(vcf):
""" Determine whether the RGQ annotation is defined in the FORMAT header of
the vcf.
-
- Since the header_iter does not return python dictionaries, we cannot easily
- test if a certain key is set, hence the ugly code.
"""
- for header in vcf.header_iter():
- try:
- header['ID']
- except KeyError:
- continue
- else:
- if header['ID'] == 'RGQ':
- return True
- return False
+ try:
+ vcf.get_header_type('RGQ')
+ except KeyError:
+ return False
+ else:
+ return True
def site_concordancy(call_vcf: VCF,
--
GitLab