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require "rgfatools.rb"
require "test/unit"
class TestRGFAToolsCopyNumber < Test::Unit::TestCase
def test_delete_low_coverage_segments
gfa = ["S\t0\t*\tRC:i:600\tLN:i:100",
"S\t1\t*\tRC:i:6000\tLN:i:100",
"S\t2\t*\tRC:i:60000\tLN:i:100"].to_rgfa
assert_equal([:"0",:"1",:"2"], gfa.segment_names)
gfa.delete_low_coverage_segments(10)
assert_equal([:"1",:"2"], gfa.segment_names)
gfa.delete_low_coverage_segments(100)
assert_equal([:"2"], gfa.segment_names)
gfa.delete_low_coverage_segments(1000)
assert_equal([], gfa.segment_names)
end
def test_compute_copy_numbers
gfa = ["S\t0\t*\tRC:i:10\tLN:i:100",
"S\t1\t*\tRC:i:1000\tLN:i:100",
"S\t2\t*\tRC:i:2000\tLN:i:100",
"S\t3\t*\tRC:i:3000\tLN:i:100"].to_rgfa
assert_nothing_raised { gfa.compute_copy_numbers(9) }
assert_equal(0, gfa.segment!("0").cn)
assert_equal(1, gfa.segment!("1").cn)
assert_equal(2, gfa.segment!("2").cn)
assert_equal(3, gfa.segment!("3").cn)
end
def test_apply_copy_number
gfa = ["S\t0\t*\tRC:i:10\tLN:i:100",
"S\t1\t*\tRC:i:1000\tLN:i:100",
"S\t2\t*\tRC:i:2000\tLN:i:100",
"S\t3\t*\tRC:i:3000\tLN:i:100"].to_rgfa
assert_equal([:"0",:"1",:"2",:"3"], gfa.segment_names)
gfa.compute_copy_numbers(9)
gfa.apply_copy_numbers
assert_equal([:"1",:"2",:"3",:"2b",:"3b",:"3c"], gfa.segment_names)
gfa.compute_copy_numbers(9)
assert(gfa.segments.map(&:cn).all?{|cn|cn == 1})
end
end
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