From 5fdc74c342c659e7a7b82184936b61a05da6949b Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 14 Nov 2011 14:56:32 +0000
Subject: [PATCH] Fix crash on variant without reference (thx Ivar)
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@418 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/variantchecker.py | 4 ++++
tests/test_variantchecker.py | 7 +++++++
2 files changed, 11 insertions(+)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index ab4f62a0..5e272e22 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1478,6 +1478,10 @@ def check_variant(description, output):
else:
record_id = parsed_description.RefSeqAcc
+ if not record_id:
+ output.addMessage(__file__, 4, 'ENOREF', 'No reference sequence given.')
+ return
+
gene_symbol = transcript_id = ''
database = Db.Cache()
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index ad15052a..2d38fcc4 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -419,3 +419,10 @@ class TestVariantchecker():
check_variant('NG_005990.1:g.1del', self.output)
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
'NG_005990.1:g.1del')
+
+ def test_no_reference(self):
+ """
+ Variant description without a reference.
+ """
+ check_variant('g.244355733del', self.output)
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOREF')), 1)
--
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