def test1(self):
r = Read(10, 50, [(0,10),(1,5),(0,10),(2,10),(0,10)])
self.assertRaisesRegexp(ValueError, 'underflows', annot.getReadOffset, r, 1)
self.assertEquals(annot.getReadOffset(r, 10), 0)
self.assertEquals(annot.getReadOffset(r, 19), 9)
self.assertEquals(annot.getReadOffset(r, 20), 15)
self.assertEquals(annot.getReadOffset(r, 29), 24)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r, 30)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r, 39)
self.assertEquals(annot.getReadOffset(r, 40), 25)
self.assertEquals(annot.getReadOffset(r, 49), 34)
self.assertRaisesRegexp(ValueError, 'overflows', annot.getReadOffset, r, 50)
def test2(self):
# qlen is set wrongly on purpose
r = Read(10, 50, [(0,10),(1,5),(0,10),(2,10),(0,10)], 30)
self.assertRaisesRegexp(ValueError, 'underflows', annot.getReadOffset, r, 1)
self.assertEquals(annot.getReadOffset(r, 10), 0)
self.assertEquals(annot.getReadOffset(r, 19), 9)
self.assertEquals(annot.getReadOffset(r, 20), 15)
self.assertEquals(annot.getReadOffset(r, 29), 24)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r, 30)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r, 39)
self.assertEquals(annot.getReadOffset(r, 40), 25)
self.assertEquals(annot.getReadOffset(r, 44), 29)
self.assertRaisesRegexp(ValueError, 'conflict', annot.getReadOffset, r, 45)
self.assertRaisesRegexp(ValueError, 'conflict', annot.getReadOffset, r, 49)
self.assertRaisesRegexp(ValueError, 'conflict', annot.getReadOffset, r, 50)
def test1(self):
r = Read(10, 50, [(0, 10), (1, 5), (0, 10), (2, 10), (0, 10)])
self.assertRaisesRegexp(ValueError, 'underflows', annot.getReadOffset,
r, 1)
self.assertEquals(annot.getReadOffset(r, 10), 0)
self.assertEquals(annot.getReadOffset(r, 19), 9)
self.assertEquals(annot.getReadOffset(r, 20), 15)
self.assertEquals(annot.getReadOffset(r, 29), 24)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r,
30)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r,
39)
self.assertEquals(annot.getReadOffset(r, 40), 25)
self.assertEquals(annot.getReadOffset(r, 49), 34)
self.assertRaisesRegexp(ValueError, 'overflows', annot.getReadOffset,
r, 50)
def test2(self):
# qlen is set wrongly on purpose
r = Read(10, 50, [(0, 10), (1, 5), (0, 10), (2, 10), (0, 10)], 30)
self.assertRaisesRegexp(ValueError, 'underflows', annot.getReadOffset,
r, 1)
self.assertEquals(annot.getReadOffset(r, 10), 0)
self.assertEquals(annot.getReadOffset(r, 19), 9)
self.assertEquals(annot.getReadOffset(r, 20), 15)
self.assertEquals(annot.getReadOffset(r, 29), 24)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r,
30)
self.assertRaisesRegexp(ValueError, 'deletion', annot.getReadOffset, r,
39)
self.assertEquals(annot.getReadOffset(r, 40), 25)
self.assertEquals(annot.getReadOffset(r, 44), 29)
self.assertRaisesRegexp(ValueError, 'conflict', annot.getReadOffset, r,
45)
self.assertRaisesRegexp(ValueError, 'conflict', annot.getReadOffset, r,
49)
self.assertRaisesRegexp(ValueError, 'conflict', annot.getReadOffset, r,
50)