pos = self.adaptor_locate_right(adaptor)
if pos > 0
- self.seq = self.seq[0 ... pos]
+ self.seq = self.seq[0 ... pos]
+ self.qual = self.qual[0 ... pos] unless self.qual.nil?
end
end
pos = self.adaptor_locate_left(adaptor)
if pos > 0
- self.seq = self.seq[pos + 1 ... self.seq.length]
+ self.seq = self.seq[pos + 1 ... self.seq.length]
+ self.qual = self.qual[pos + 1 ... self.qual.length] unless self.qual.nil?
end
end
assert_equal( "nnnnn", @entry.seq)
end
+ def test_Seq_adaptor_clip_right_returns_correct_qual
+ @entry.seq = "nnnnncgat"
+ @entry.qual = "abcdefghi"
+ @entry.adaptor_clip_right("cgat")
+ assert_equal( "abcde", @entry.qual)
+ end
+
def test_Seq_adaptor_clip_left_returns_correct_sequence
@entry.seq = "cgatnnnnn"
@entry.adaptor_clip_left("cgat")
assert_equal( "nnnnn", @entry.seq)
end
+ def test_Seq_adaptor_clip_left_returns_correct_qual
+ @entry.seq = "cgatnnnnn"
+ @entry.qual = "abcdefghi"
+ @entry.adaptor_clip_left("cgat")
+ assert_equal( "efghi", @entry.qual)
+ end
+
def test_Digest_new_raises_on_bad_pattern_residue
assert_raise(DigestError) { Digest.new(@entry, "X", 4) }
end