def test_ends_just_before_insertion(self):
al = pysam.AlignedSegment()
al.reference_start = 100
al.cigar = [(MATCH, 50), (INS, 10), (MATCH, 50)]
al.seq = 'A' * 110
cropped = pysam.AlignedSegment()
cropped.reference_start = 100
cropped.cigar = [(MATCH, 50), (SOFT_CLIP, 60)]
cropped.seq = 'A' * 110
output = sam.crop_al_to_ref_int(al, 100, 149)
self.assertEqual(output, cropped)
output = sam.crop_al_to_ref_int(al, 100, 150)
self.assertNotEqual(output, cropped)
def test_ends_in_deletion(self):
al = pysam.AlignedSegment()
al.reference_start = 100
al.cigar = [(MATCH, 50), (DEL, 10), (MATCH, 50)]
al.seq = 'A' * 100
cropped = pysam.AlignedSegment()
cropped.reference_start = 100
cropped.cigar = [(MATCH, 50), (SOFT_CLIP, 50)]
cropped.seq = 'A' * 100
output = sam.crop_al_to_ref_int(al, 100, 155)
self.assertEqual(output, cropped)
output = sam.crop_al_to_ref_int(al, 100, 160)
self.assertNotEqual(output, cropped)
def test_starts_just_before_deletion(self):
al = pysam.AlignedSegment()
al.reference_start = 100
al.cigar = [(MATCH, 50), (DEL, 10), (MATCH, 50)]
al.seq = 'A' * 100
cropped = pysam.AlignedSegment()
cropped.reference_start = 149
cropped.cigar = [(SOFT_CLIP, 49), (MATCH, 1), (DEL, 10), (MATCH, 50)]
cropped.seq = 'A' * 100
output = sam.crop_al_to_ref_int(al, 149, 210)
self.assertEqual(output, cropped)
output = sam.crop_al_to_ref_int(al, 150, 210)
self.assertNotEqual(output, cropped)
def test_simple(self):
al = pysam.AlignedSegment()
al.reference_start = 100
al.cigar = [(MATCH, 100)]
al.seq = 'A' * 100
cropped = pysam.AlignedSegment()
cropped.reference_start = 150
cropped.cigar = [(SOFT_CLIP, 50), (MATCH, 10), (SOFT_CLIP, 40)]
cropped.seq = 'A' * 100
output = sam.crop_al_to_ref_int(al, 150, 159)
self.assertEqual(output, cropped)
output = sam.crop_al_to_ref_int(al, 150, 158)
self.assertNotEqual(output, cropped)