From 5952b8a0d008ad85e736d6e89c7b31e4a9830922 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Thu, 26 Jul 2012 14:35:20 +0000
Subject: [PATCH] Removed erroneous optional argument check for DelIns. (Fixes
#108).
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@589 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/variantchecker.py | 10 +++-------
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index f563a55b..ffe9baef 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -607,7 +607,7 @@ def apply_insertion(before, after, s, mutator, record, O):
#apply_insertion
-def apply_delins(first, last, delete, insert, mutator, record, output):
+def apply_delins(first, last, insert, mutator, record, output):
"""
Do a semantic check for an delins, do the actual delins, and give
it a name.
@@ -616,9 +616,6 @@ def apply_delins(first, last, delete, insert, mutator, record, output):
@type first: int
@arg last: Genomic end position of the delins.
@type last: int
- @arg delete: Sequence to delete (may be None, in which case it will be
- constructed from the reference sequence).
- @type delete: string
@arg insert: Sequence to insert.
@type insert: string
@arg mutator: A Mutator instance.
@@ -628,8 +625,7 @@ def apply_delins(first, last, delete, insert, mutator, record, output):
@arg output: The Output object.
@type output: Modules.Output.Output
"""
- if not delete:
- delete = mutator.orig[first - 1:last]
+ delete = mutator.orig[first - 1:last]
if str(delete) == str(insert):
output.addMessage(__file__, 2, 'WNOCHANGE',
@@ -1187,7 +1183,7 @@ def process_raw_variant(mutator, variant, record, transcript, output):
output.addMessage(__file__, 4, 'ENOTIMPLEMENTED',
'Insertion of a range is not implemented yet.')
raise _RangeInsertionError()
- apply_delins(first, last, argument, sequence, mutator, record, output)
+ apply_delins(first, last, sequence, mutator, record, output)
#process_raw_variant
--
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