def test_partition_cigar_refNonconsumingOps(self):
util = cigar.CigarUtil(42, "5M4I1M")
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(42,""), c1)
self.assertEquals(cigar.CigarUtil(42,"5M"), c2)
self.assertEquals(cigar.CigarUtil(47,"4I1M"), c3)
(c1, c2, c3) = util._partition_cigar(47, 48)
self.assertEquals(cigar.CigarUtil(42,"5M"), c1)
self.assertEquals(cigar.CigarUtil(47,"4I1M"), c2)
self.assertEquals(cigar.CigarUtil(48,""), c3)
def test_partition_cigar_refNonconsumingOps(self):
util = cigar.CigarUtil(42, "5M4I1M")
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(42, ""), c1)
self.assertEquals(cigar.CigarUtil(42, "5M"), c2)
self.assertEquals(cigar.CigarUtil(47, "4I1M"), c3)
(c1, c2, c3) = util._partition_cigar(47, 48)
self.assertEquals(cigar.CigarUtil(42, "5M"), c1)
self.assertEquals(cigar.CigarUtil(47, "4I1M"), c2)
self.assertEquals(cigar.CigarUtil(48, ""), c3)
def test_partition_cigar_refNonconsumingOpsWithFlankingSoftclips(self):
util = cigar.CigarUtil(42, "5S" "5M" "4I" "1M" "5S")
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(37, "5S"), c1)
self.assertEquals(cigar.CigarUtil(42, "5M"), c2)
self.assertEquals(cigar.CigarUtil(47, "4I1M5S"), c3)
(c1, c2, c3) = util._partition_cigar(47, 48)
self.assertEquals(cigar.CigarUtil(37, "5S5M"), c1)
self.assertEquals(cigar.CigarUtil(47, "4I1M"), c2)
self.assertEquals(cigar.CigarUtil(48, "5S"), c3)
(c1, c2, c3) = util._partition_cigar(48, 53)
self.assertEquals(cigar.CigarUtil(37, "5S5M4I1M"), c1)
self.assertEquals(cigar.CigarUtil(48, "5S"), c2)
self.assertEquals(cigar.CigarUtil(53, ""), c3)
def test_partition_cigar_refConsumingOps(self):
util = cigar.CigarUtil(42, "5M5X")
# | 4444444455
# | 2345678901
# | MMMMM
# | XXXXX
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(42, ""), c1)
self.assertEquals(cigar.CigarUtil(42, "5M"), c2)
self.assertEquals(cigar.CigarUtil(47, "5X"), c3)
(c1, c2, c3) = util._partition_cigar(47, 52)
self.assertEquals(cigar.CigarUtil(42, "5M"), c1)
self.assertEquals(cigar.CigarUtil(47, "5X"), c2)
self.assertEquals(cigar.CigarUtil(52, ""), c3)
def test_partition_cigar_refNonconsumingOpsWithFlankingSoftclips(self):
util = cigar.CigarUtil(42, "5S" "5M" "4I" "1M" "5S")
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(37,"5S"), c1)
self.assertEquals(cigar.CigarUtil(42,"5M"), c2)
self.assertEquals(cigar.CigarUtil(47,"4I1M5S"), c3)
(c1, c2, c3) = util._partition_cigar(47, 48)
self.assertEquals(cigar.CigarUtil(37,"5S5M"), c1)
self.assertEquals(cigar.CigarUtil(47,"4I1M"), c2)
self.assertEquals(cigar.CigarUtil(48,"5S"), c3)
(c1, c2, c3) = util._partition_cigar(48, 53)
self.assertEquals(cigar.CigarUtil(37,"5S5M4I1M"), c1)
self.assertEquals(cigar.CigarUtil(48,"5S"), c2)
self.assertEquals(cigar.CigarUtil(53,""), c3)
def test_partition_cigar_refConsumingOps(self):
util = cigar.CigarUtil(42, "5M5X")
# | 4444444455
# | 2345678901
# | MMMMM
# | XXXXX
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(42,""), c1)
self.assertEquals(cigar.CigarUtil(42,"5M"), c2)
self.assertEquals(cigar.CigarUtil(47,"5X"), c3)
(c1, c2, c3) = util._partition_cigar(47, 52)
self.assertEquals(cigar.CigarUtil(42,"5M"), c1)
self.assertEquals(cigar.CigarUtil(47,"5X"), c2)
self.assertEquals(cigar.CigarUtil(52,""), c3)
def test_partition_cigar_targetRegionBoundedByShortReverseRead(self):
util = cigar.CigarUtil(100, "20M")
(c1, c2, c3) = util._partition_cigar(90, 120)
self.assertEquals(100, c1.reference_start)
self.assertEquals("", c1.cigar)
self.assertEquals(100, c2.reference_start)
self.assertEquals("20M", c2.cigar)
self.assertEquals(120, c3.reference_start)
self.assertEquals("", c3.cigar)
def test_partition_cigar_targetRegionBoundedByShortReverseRead(self):
util = cigar.CigarUtil(100, "20M")
(c1, c2, c3) = util._partition_cigar(90, 120)
self.assertEquals(100, c1.reference_start)
self.assertEquals("", c1.cigar)
self.assertEquals(100, c2.reference_start)
self.assertEquals("20M", c2.cigar)
self.assertEquals(120, c3.reference_start)
self.assertEquals("", c3.cigar)
def test_partition_outOfBounds(self):
# ref | 4444444444
# | 0123456789
# read | SSMMMMMXX
# index | 210123456
util = cigar.CigarUtil(42, "2S" "6M" "2X")
(c1, c2, c3) = util._partition_cigar(30, 42)
self.assertEquals(cigar.CigarUtil(40, ""), c1)
self.assertEquals(cigar.CigarUtil(40, "2S"), c2)
self.assertEquals(cigar.CigarUtil(42, "6M2X"), c3)
(c1, c2, c3) = util._partition_cigar(48, 60)
self.assertEquals(cigar.CigarUtil(40, "2S6M"), c1)
self.assertEquals(cigar.CigarUtil(48, "2X"), c2)
self.assertEquals(cigar.CigarUtil(50, ""), c3)
(c1, c2, c3) = util._partition_cigar(20, 30)
self.assertEquals(cigar.CigarUtil(40, ""), c1)
self.assertEquals(cigar.CigarUtil(40, ""), c2)
self.assertEquals(cigar.CigarUtil(40, "2S6M2X"), c3)
(c1, c2, c3) = util._partition_cigar(100, 110)
self.assertEquals(cigar.CigarUtil(40, "2S6M2X"), c1)
self.assertEquals(cigar.CigarUtil(50, ""), c2)
self.assertEquals(cigar.CigarUtil(50, ""), c3)
def test_partition_outOfBounds(self):
# ref | 4444444444
# | 0123456789
# read | SSMMMMMXX
# index | 210123456
util = cigar.CigarUtil(42, "2S" "6M" "2X")
(c1, c2, c3) = util._partition_cigar(30, 42)
self.assertEquals(cigar.CigarUtil(40,""), c1)
self.assertEquals(cigar.CigarUtil(40,"2S"), c2)
self.assertEquals(cigar.CigarUtil(42,"6M2X"), c3)
(c1, c2, c3) = util._partition_cigar(48, 60)
self.assertEquals(cigar.CigarUtil(40,"2S6M"), c1)
self.assertEquals(cigar.CigarUtil(48,"2X"), c2)
self.assertEquals(cigar.CigarUtil(50,""), c3)
(c1, c2, c3) = util._partition_cigar(20, 30)
self.assertEquals(cigar.CigarUtil(40,""), c1)
self.assertEquals(cigar.CigarUtil(40,""), c2)
self.assertEquals(cigar.CigarUtil(40,"2S6M2X"), c3)
(c1, c2, c3) = util._partition_cigar(100, 110)
self.assertEquals(cigar.CigarUtil(40,"2S6M2X"), c1)
self.assertEquals(cigar.CigarUtil(50,""), c2)
self.assertEquals(cigar.CigarUtil(50,""), c3)
def test_partition_cigar(self):
util = cigar.CigarUtil(42, "2S" "6M" "2S")
(c1, c2, c3) = util._partition_cigar(42, 48)
self.assertEquals(cigar.CigarUtil(40, "2S"), c1)
self.assertEquals(cigar.CigarUtil(42, "6M"), c2)
self.assertEquals(cigar.CigarUtil(48, "2S"), c3)
def test_partition_cigar(self):
util = cigar.CigarUtil(42, "2S" "6M" "2S")
(c1, c2, c3) = util._partition_cigar(42, 48)
self.assertEquals(cigar.CigarUtil(40,"2S"), c1)
self.assertEquals(cigar.CigarUtil(42,"6M"), c2)
self.assertEquals(cigar.CigarUtil(48,"2S"), c3)