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require "rgfa.rb"
require "test/unit"
class TestRGFALineSegment < Test::Unit::TestCase
def test_from_string
fields=["S","1","ACGTCACANNN","RC:i:1232","LN:i:11","ab:Z:abcd",
"FC:i:2321","KC:i:1212"]
str=fields.join("\t")
assert_nothing_raised { str.to_rgfa_line }
assert_equal(RGFA::Line::Segment, 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.name)
assert_equal(fields[2], str.to_rgfa_line.sequence)
assert_equal(1232, str.to_rgfa_line.RC)
assert_equal(11, str.to_rgfa_line.LN)
assert_equal(2321, str.to_rgfa_line.FC)
assert_equal(1212, str.to_rgfa_line.KC)
assert_equal("abcd", str.to_rgfa_line.ab)
assert_raises(RGFA::FieldParser::FormatError) { (str+"\tH1").to_rgfa_line }
assert_raises(RGFA::Line::RequiredFieldMissingError) { "S\tH".to_rgfa_line }
assert_raises(RGFA::FieldParser::FormatError) do
f=fields.dup; f[2]="!@#?"; f.join("\t").to_rgfa_line(validate: 3)
end
assert_raises(RGFA::Line::PredefinedOptfieldTypeError) do
f=fields.dup; f[3]="RC:Z:1232"; f.join("\t").to_rgfa_line
end
f=["S","2","ACGTCACANNN","LN:i:3"]
assert_raises(RGFA::Line::Segment::InconsistentLengthError) do
f.join("\t").to_rgfa_line(validate: 3)
end
f=["S","2","ACGTCACANNN","LN:i:11"]
assert_nothing_raised { f.join("\t").to_rgfa_line }
f=["S","2","*","LN:i:3"]
assert_nothing_raised { f.join("\t").to_rgfa_line }
end
def test_forbidden_segment_names
assert_nothing_raised { "S\tA+B\t*".to_rgfa_line }
assert_nothing_raised { "S\tA-B\t*".to_rgfa_line }
assert_nothing_raised { "S\tA,B\t*".to_rgfa_line }
assert_raises(RGFA::FieldParser::FormatError) do
"S\tA+,B\t*".to_rgfa_line
end
assert_raises(RGFA::FieldParser::FormatError) do
"S\tA-,B\t*".to_rgfa_line
end
end
def test_coverage
l = "S\t0\t*\tRC:i:600\tLN:i:100".to_rgfa_line
assert_equal(6, l.coverage)
assert_equal(6, l.coverage!)
l = "S\t0\t*\tRC:i:600".to_rgfa_line
assert_equal(nil, l.coverage)
assert_raises(RGFA::Line::Segment::UndefinedLengthError) {l.coverage!}
l = "S\t0\t*\tLN:i:100".to_rgfa_line
assert_equal(nil, l.coverage)
assert_raises(RGFA::Line::TagMissingError) {l.coverage!}
l = "S\t0\t*\tFC:i:600\tLN:i:100".to_rgfa_line
assert_equal(nil, l.coverage)
assert_raises(RGFA::Line::TagMissingError) {l.coverage!}
assert_equal(6, l.coverage(count_tag: :FC))
assert_equal(6, l.coverage!(count_tag: :FC))
end
def test_other_orientation
assert_equal(:+, RGFA::OrientedSegment.invert("-"))
assert_equal(:-, RGFA::OrientedSegment.invert("+"))
assert_equal(:-, RGFA::OrientedSegment.invert(:+))
assert_raises(RGFA::SegmentInfo::InvalidAttributeError) do
RGFA::OrientedSegment.invert("x")
end
end
end
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