def test_softclip_target_flankingSoftclips(self):
util = cigar.CigarUtil(42, "2S" "6M" "2S")
# 4444444444
# 0123456789
# SSMMMMMMSS
# SSSMMMMSSS
new_util = util.softclip_target(43, 47)
self.assertEquals("3S4M3S", new_util.cigar)
self.assertEquals(43, new_util.reference_start)
def test_softclip_target_flankingHardclips(self):
util = cigar.CigarUtil(42, "2H1S" "4M" "1S2H")
#3444444444
#9012345678
#HHSMMMMSHH
#HHSSMMSSHH
new_util = util.softclip_target(43, 45)
self.assertEquals("2H2S" "2M" "2S2H", new_util.cigar)
self.assertEquals(43, new_util.reference_start)
def test_softclip_target_flankingHardclips(self):
util = cigar.CigarUtil(42, "2H1S" "4M" "1S2H")
#3444444444
#9012345678
#HHSMMMMSHH
#HHSSMMSSHH
new_util = util.softclip_target(43,45)
self.assertEquals("2H2S" "2M" "2S2H", new_util.cigar)
self.assertEquals(43, new_util.reference_start)
def test_softclip_target_flankingSoftclips(self):
util = cigar.CigarUtil(42, "2S" "6M" "2S")
# 4444444444
# 0123456789
# SSMMMMMMSS
# SSSMMMMSSS
new_util = util.softclip_target(43,47)
self.assertEquals("3S4M3S", new_util.cigar)
self.assertEquals(43, new_util.reference_start)
def test_softclip_target_deletes(self):
util = cigar.CigarUtil(42, "2M3D" "4M" "1S")
#4444444455
#2345678901
#MMDDD
# MMMM
# S
#SS MMMMS
new_util = util.softclip_target(47, 51)
self.assertEquals("2S" "4M" "1S", new_util.cigar)
self.assertEquals(47, new_util.reference_start)
def test_softclip_target_deletes(self):
util = cigar.CigarUtil(42, "2M3D" "4M" "1S")
#4444444455
#2345678901
#MMDDD
# MMMM
# S
#SS MMMMS
new_util = util.softclip_target(47,51)
self.assertEquals("2S" "4M" "1S", new_util.cigar)
self.assertEquals(47, new_util.reference_start)
def test_softclip_target_edgeDelete(self):
util = cigar.CigarUtil(42, "3M" "1D5M" "2S")
#44444444555
#23456789012
#ATA ACGTACG
#MMM
# DMMMM
# MSS
#SSS MMMMSSS
new_util = util.softclip_target(45, 50)
self.assertEquals("3S" "4M" "3S", new_util.cigar)
self.assertEquals(46, new_util.reference_start)
def test_softclip_target_edgeInsert(self):
util = cigar.CigarUtil(42, "3M" "1I4M" "2X")
#444 444445
#234 567890
#ATAAACGTAC
#MMMI
# MMMM
# XX
#SSSSMMMMSS
new_util = util.softclip_target(45, 49)
self.assertEquals("4S" "4M" "2S", new_util.cigar)
self.assertEquals(45, new_util.reference_start)
def test_softclip_target_edgeDelete(self):
util = cigar.CigarUtil(42, "3M" "1D5M" "2S")
#44444444555
#23456789012
#ATA ACGTACG
#MMM
# DMMMM
# MSS
#SSS MMMMSSS
new_util = util.softclip_target(45,50)
self.assertEquals("3S" "4M" "3S", new_util.cigar)
self.assertEquals(46, new_util.reference_start)
def test_softclip_target_edgeInsert(self):
util = cigar.CigarUtil(42, "3M" "1I4M" "2X")
#444 444445
#234 567890
#ATAAACGTAC
#MMMI
# MMMM
# XX
#SSSSMMMMSS
new_util = util.softclip_target(45,49)
self.assertEquals("4S" "4M" "2S", new_util.cigar)
self.assertEquals(45, new_util.reference_start)
def test_softclip_target(self):
util = cigar.CigarUtil(42, "10M")
new_util = util.softclip_target(44, 50)
self.assertEquals("2S6M2S", new_util.cigar)
self.assertEquals(44, new_util.reference_start)
def test_softclip_target(self):
util = cigar.CigarUtil(42, "10M")
new_util = util.softclip_target(44,50)
self.assertEquals("2S6M2S", new_util.cigar)
self.assertEquals(44, new_util.reference_start)
