diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py index f563a55bfa073cdb6368ebf1552095998963541c..ffe9baef0e75ac1b4fe5940af061248a76503a9e 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