1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
require "rgfa.rb"
require "test/unit"
class TestRGFALinePath < Test::Unit::TestCase
def test_from_string
fields=["P","4","1+,2-,3+","9M2I3D1M,12M","ab:Z:abcd"]
str=fields.join("\t")
assert_nothing_raised { str.to_rgfa_line }
assert_equal(RGFA::Line::Path, str.to_rgfa_line.class)
assert_equal(fields[0].to_sym, str.to_rgfa_line.record_type)
assert_equal(fields[1].to_sym, str.to_rgfa_line.path_name)
assert_equal([[:"1",:"+"],[:"2",:"-"],[:"3",:"+"]],
str.to_rgfa_line.segment_names)
assert_equal([[RGFA::CIGAR::Operation.new(9,:M),
RGFA::CIGAR::Operation.new(2,:I),
RGFA::CIGAR::Operation.new(3,:D),
RGFA::CIGAR::Operation.new(1,:M)],
[RGFA::CIGAR::Operation.new(12,:M)]],
str.to_rgfa_line.overlaps)
assert_equal("abcd", str.to_rgfa_line.ab)
assert_raises(RGFA::FieldParser::FormatError) { (str+"\tH1").to_rgfa_line }
assert_raises(RGFA::Line::RequiredFieldMissingError) { "P\tH".to_rgfa_line }
assert_raises(RGFA::FieldParser::FormatError) do
f=fields.dup; f[2]="1,2,3"; f.join("\t").to_rgfa_line(validate: 3)
end
assert_raises(RGFA::Line::Path::ListLengthsError) do
f=fields.dup; f[2]="1+"; f.join("\t").to_rgfa_line(validate: 3)
end
assert_nothing_raised do
f=fields.dup; f[3]="*,*"; f.join("\t").to_rgfa_line(validate: 3)
end
assert_nothing_raised do
f=fields.dup; f[3]="9M2I3D1M,12M,12M"; f.join("\t").
to_rgfa_line(validate: 3)
end
assert_nothing_raised do
f=fields.dup; f[3]="*"; f.join("\t").to_rgfa_line(validate: 3)
end
assert_raises(RGFA::CIGAR::ValueError) do
f=fields.dup; f[3]="12,12"; f.join("\t").to_rgfa_line(validate: 3)
end
assert_raises(RGFA::CIGAR::ValueError) do
f=fields.dup; f[3]="12M|12M"; f.join("\t").to_rgfa_line(validate: 3)
end
end
end
|
