def find_all_rv_variantkey_by_rsid(self, rsid):
"""Search for the specified rsID and returns all associated VariantKeys.
Parameters
----------
rsid : uint32
rsID to search.
Returns
-------
uint64 :
- VariantKey(s).
"""
vk = []
rsid_arr = np.array(rsid).astype(np.uint32)
for x in np.nditer(rsid_arr):
vk = vk + pvk.find_all_rv_variantkey_by_rsid(
self.rsvk_mc, 0, self.rsvk_nrows, x.item(0))
return np.array(vk).astype(np.uint64)
def test_find_all_rv_variantkey_by_rsid(self):
vks = bs.find_all_rv_variantkey_by_rsid(rvmsrc, 0, 9, 0x00000003)
self.assertEqual(len(vks), 3)
self.assertEqual(vks[0], 0x80010274003A0000)
self.assertEqual(vks[1], 0x8001028D00138000)
self.assertEqual(vks[2], 0x80010299007A0000)
def test_find_all_rv_variantkey_by_rsid_notfound(self):
vks = bs.find_all_rv_variantkey_by_rsid(rvmsrc, 0, 9, 0xfffffff0)
self.assertEqual(len(vks), 0)
vk.get_next_rv_variantkey_by_rsid(mc, 2, nrows, 0x00000061)
# (9223656209074749440, 3)
vk.munmap_binfile(mf)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Load the lookup table for rsID to VariantKey.
# The input binary file can be generated using the resources/tools/rsvk.sh script.
# This example uses the "c/test/data/rsvk.m.10.bin".
mf, mc, nrows = vk.mmap_rsvk_file('rsvk.m.10.bin', [])
if nrows <= 0:
assert False, "Unable to open the rsvk.m.10.bin file"
vk.find_all_rv_variantkey_by_rsid(mc, 0, nrows, 0x00000003)
# [9223656209074749440, 9223656316446408704, 9223656367992733696]
vk.munmap_binfile(mf)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Load the lookup table for VariantKey ro rsID
# The input binary file can be generated using the resources/tools/vkrs.sh script.
# This example uses the "c/test/data/vkrs.10.bin".
mf, mc, nrows = vk.mmap_vkrs_file('vkrs.10.bin', [])
if nrows <= 0:
assert False, "Unable to open the vkrs.10.bin file"
vk.find_vr_rsid_by_variantkey(mc, 0, nrows, vk=0X80010274003A0000)
# (97, 3)
print(vk.get_next_rv_variantkey_by_rsid(mfsrc, 2, 9, 0x00000061))
# (9223656209074749440, 3)
vk.munmap_binfile(mfsrc, mffd, mfsize)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Load the lookup table for rsID to VariantKey.
# The input binary file can be generated using the resources/tools/vkhexbin.sh script.
# This example uses the "c/test/data/rsvk.m.10.bin".
mfsrc, mffd, mfsize, mflast = vk.mmap_binfile('rsvk.m.10.bin')
if mffd < 0:
assert False, "Unable to open the rsvk.m.10.bin file"
print(vk.find_all_rv_variantkey_by_rsid(mfsrc, 0, 9, 0x00000003))
# [9223656209074749440, 9223656316446408704, 9223656367992733696]
vk.munmap_binfile(mfsrc, mffd, mfsize)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Load the lookup table for VariantKey ro rsID
# The input binary file can be generated using the resources/tools/vkhexbin.sh script.
# This example uses the "c/test/data/vkrs.10.bin".
mfsrc, mffd, mfsize, mflast = vk.mmap_binfile('vkrs.10.bin')
if mffd < 0:
assert False, "Unable to open the vkrs.10.bin file"
print(vk.get_vr_rsid(mfsrc, item=3))
# 97
