def test_get_variantkey_ref_length_not_found(self):
osizeref = bs.get_variantkey_ref_length(mc, 0xffffffffffffffff)
self.assertEqual(osizeref, 0)
def test_get_variantkey_ref_length_reversible(self):
osizeref = bs.get_variantkey_ref_length(mc, 0x1800925199160000)
self.assertEqual(osizeref, 3)
# The VCF file can be normalized using the `resources/tools/vcfnorm.sh` script.
# This example uses the "c/test/data/nrvk.10.bin".
mf, mc, nrows = vk.mmap_nrvk_file('nrvk.10.bin')
if nrows <= 0:
assert False, "Unable to open the nrvk.10.bin file"
vk.find_ref_alt_by_variantkey(mc, vk=0x2000c3521f1c15ab)
# (b'ACGTACGT', b'ACGT', 8, 4, 12)
# Return values are: REF, ALT, REF length, ALT length, REF+ALT length
# Reverse all VariantKeys, including the ones that are not directly reversible by using a lookup table.
vk.reverse_variantkey(mc, vk=0x2000c3521f1c15ab)
# (b'4', 100004, b'ACGTACGT', b'ACGT', 8, 4, 12)
# Return values are: CHROM, POS, REF, ALT, REF length, ALT length, REF+ALT length
vk.get_variantkey_ref_length(mc, vk=0x2000c3521f1c15ab)
# 8
vk.get_variantkey_endpos(mc, vk=0x2000c3521f1c15ab)
# 100012
vk.get_variantkey_chrom_startpos(vk=0x2000c3521f1c15ab)
# 1073841828
vk.get_variantkey_chrom_endpos(mc, vk=0x2000c3521f1c15ab)
# 1073841836
vk.munmap_binfile(mf)
# /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
def test_get_variantkey_ref_length(self):
for vkey, chrom, pos, ralen, sizeref, sizealt, csp, cep, ref, alt in testData:
osizeref = bs.get_variantkey_ref_length(mc, vkey)
self.assertEqual(osizeref, sizeref)
# The VCF file can be normalized using the `resources/tools/vcfnorm.sh` script.
# This example uses the "c/test/data/vknr.10.bin".
mfsrc, mffd, mfsize, mflast = vk.mmap_binfile('vknr.10.bin')
if mffd < 0:
assert False, "Unable to open the vknr.10.bin file"
print(vk.find_ref_alt_by_variantkey(mfsrc, mflast, vk=0x2000c3521f1c15ab))
# (b'ACGTACGT', b'ACGT', 8, 4, 12)
# Return values are: REF, ALT, REF length, ALT length, REF+ALT length
# Reverse all VariantKeys, including the ones that are not directly reversible by using a lookup table.
print(vk.reverse_variantkey(mfsrc, mflast, vk=0x2000c3521f1c15ab))
# (b'4', 100004, b'ACGTACGT', b'ACGT', 8, 4, 12)
# Return values are: CHROM, POS, REF, ALT, REF length, ALT length, REF+ALT length
print(vk.get_variantkey_ref_length(mfsrc, mflast, vk=0x2000c3521f1c15ab))
# 8
print(vk.get_variantkey_endpos(mfsrc, mflast, vk=0x2000c3521f1c15ab))
# 100012
print(vk.get_variantkey_chrom_startpos(vk=0x2000c3521f1c15ab))
# 1073841828
print(vk.get_variantkey_chrom_endpos(mfsrc, mflast, vk=0x2000c3521f1c15ab))
# 1073841836
vk.munmap_binfile(mfsrc, mffd, mfsize)
# /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\