def test_bgen_samples_outside_bgen_unreadable(tmp_path):
bgen_filepath = example_filepath2("complex.23bits.bgen")
samples_filepath = tmp_path / "complex.sample"
copyfile(example_filepath("complex.sample"), samples_filepath)
with noread_permission(samples_filepath):
with pytest.raises(PermissionError):
open_bgen(bgen_filepath, samples_filepath=samples_filepath, allow_complex=True, verbose=False)
def test_allele_expectation():
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
e = bgen2.allele_expectation(np.s_[bgen2.samples == "sample_005",
bgen2.rsids == "RSID_6"])
assert np.allclose(e, [[[1.01086423, 0.98913577]]])
with pytest.raises(ValueError):
filepath = example_filepath("haplotypes.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
bgen2.allele_expectation()
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
e = bgen2.allele_expectation(np.s_[:, []])
assert e.shape == (500, 0, 2)
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
e = bgen2.allele_expectation(
np.s_[bgen2.samples == "sample_005", bgen2.rsids == "RSID_6"],
assume_constant_ploidy=False,
)
assert np.allclose(e, [[[1.01086423, 0.98913577]]])
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
e = bgen2.allele_expectation(np.s_[:, []],
assume_constant_ploidy=False)
assert e.shape == (500, 0, 2)
def test_to_improve_coverage2():
filepath = example_filepath2("complex.bgen")
samplepath = example_filepath2("complex.sample")
allow_complex = True
metadata2_path = open_bgen._metadata_path_from_filename(
filepath, samples_filepath=samplepath, allow_complex=allow_complex)
if metadata2_path.exists():
metadata2_path.unlink()
metadata2_temp = metadata2_path.parent / (metadata2_path.name + ".temp")
metadata2_temp.touch() # Create an empty .temp file
bgen2 = open_bgen(
filepath,
samples_filepath=samplepath,
allow_complex=allow_complex,
verbose=True,
) # Creates metadata2.mmm file
bgen2 = open_bgen(
filepath,
samples_filepath=samplepath,
allow_complex=True,
verbose=True,
) # Creates metadata2.mmm file
del bgen2
def test_close_del_with():
filepath = example_filepath2("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
pass
with pytest.raises(ValueError):
bgen2.read()
bgen2 = open_bgen(filepath, verbose=False)
bgen2.close()
with pytest.raises(ValueError):
bgen2.read()
def test_open_bgen_phased_genotype():
filepath = example_filepath2("haplotypes.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
assert_equal(bgen2.chromosomes[0], "1")
assert_equal(bgen2.ids[0], "SNP1")
assert_equal(bgen2.nalleles[0], 2)
assert_equal(bgen2.allele_ids[0], "A,G")
assert_equal(bgen2.positions[0], 1)
assert_equal(bgen2.rsids[0], "RS1")
assert_equal(bgen2.chromosomes[2], "1")
assert_equal(bgen2.ids[2], "SNP3")
assert_equal(bgen2.nalleles[2], 2)
assert_equal(bgen2.allele_ids[2], "A,G")
assert_equal(bgen2.positions[2], 3)
assert_equal(bgen2.rsids[2], "RS3")
assert_equal(bgen2.samples[0], "sample_0")
assert_equal(bgen2.samples[2], "sample_2")
assert_equal(bgen2.samples[-1], "sample_3")
g = bgen2.read((0, 0))
assert_allclose(g[0, 0, :], [1.0, 0.0, 1.0, 0.0])
g = bgen2.read((-1, -1))
assert_allclose(g[0, 0, :], [1.0, 0.0, 0.0, 1.0])
def random_file_tests(nsamples,
nvariants,
bits,
verbose=False,
overwrite=False):
test_data_folder = BGEN_READER_CACHE_HOME / "test_data"
filepath = test_data_folder / "{0}x{1}.{2}bits.bgen".format(
nsamples, nvariants, bits)
if overwrite or not filepath.exists():
_write_random(
filepath,
nsamples,
nvariants,
bits=bits,
verbose=verbose,
cleanup_temp_files=True,
)
metadata2_path = open_bgen._metadata_path_from_filename(
filepath, samples_filepath=None, allow_complex=True)
if metadata2_path.exists():
metadata2_path.unlink()
with open_bgen(filepath, verbose=verbose) as bgen2:
assert bgen2.nsamples == nsamples
assert bgen2.nvariants == nvariants
val = bgen2.read(-1)
assert val.shape == (nsamples, 1, 3)
mean = np.nanmean(val)
assert mean != mean or (0 <= mean and mean <= 1)
def test_custom_meta_path():
filepath = example_filepath2("example.bgen")
custom_path = Path(BGEN_READER_CACHE_HOME, "submeta")
try:
os.mkdir(custom_path)
except FileExistsError:
pass
custom_meta_path(custom_path)
read_bgen(filepath)
open_bgen(filepath)
assert len([path for path in Path(custom_path).iterdir()]) == 2, "Failed to write files to custom directory"
os.remove(Path(custom_path, filepath.name + ".metadata2.mmm"))
os.remove(Path(custom_path, filepath.name + ".metafile"))
def test_dosage_example_32bits():
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen:
e = bgen.allele_expectation([5, 0])
assert_allclose(e[7, 0, :], [1.9556273911044997, 0.044372608895500334])
assert all(isnan(e[0, 1, :]))
assert_equal(e.shape, (500, 2, 2))
def test_bgen_file_not_readable(tmp_path):
filepath = tmp_path / "haplotypes.bgen"
copyfile(example_filepath2("haplotypes.bgen"), filepath)
with noread_permission(filepath):
with pytest.raises(PermissionError):
with open_bgen(filepath, verbose=False) as _:
pass
def test_zero_width():
filepath = example_filepath("complex.bgen")
with open_bgen(filepath, allow_complex=True, verbose=False) as bgen:
for assume_constant_ploidy in [False, True]:
e = bgen.allele_expectation(
[],
assume_constant_ploidy=assume_constant_ploidy,
)
f = bgen.allele_frequency(e)
assert e.shape == (bgen.nsamples, 0, bgen.nalleles[0])
assert f.shape == (0, bgen.nalleles[0])
good_variants = logical_not(bgen.phased) * (bgen.nalleles == 2)
e = bgen.allele_expectation(
([], good_variants),
assume_constant_ploidy=assume_constant_ploidy,
)
f = bgen.allele_frequency(e)
assert e.shape == (0, sum(good_variants), bgen.nalleles[0])
assert_equal(f, zeros(
(sum(good_variants), bgen.nalleles[0]
))) # We define the freq of something with no samples as 0
e = bgen.allele_expectation(
([], []),
assume_constant_ploidy=assume_constant_ploidy,
)
f = bgen.allele_frequency(e)
assert e.shape == (0, 0, bgen.nalleles[0])
assert f.shape == (0, bgen.nalleles[0])
def test_read_multiple_returns():
filepath = example_filepath2("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
full, full_missing, full_ploidy = bgen2.read(return_missings=True,
return_ploidies=True)
val, missing = bgen2.read(return_missings=True)
assert np.allclose(full, val, equal_nan=True)
assert np.allclose(full_missing, missing, equal_nan=False)
ploidy = bgen2.read(return_probabilities=False, return_ploidies=True)
assert np.allclose(full_ploidy, ploidy, equal_nan=False)
val, missing = bgen2.read((slice(10, 30, 2), [11, 9]),
return_missings=True)
assert np.allclose(full[10:30:2, :][:, [11, 9]], val, equal_nan=True)
assert np.allclose(full_missing[10:30:2, :][:, [11, 9]],
missing,
equal_nan=False)
ploidy = bgen2.read(
(slice(10, 30, 2), [11, 9]),
return_probabilities=False,
return_ploidies=True,
)
assert np.allclose(full_ploidy[10:30:2, :][:, [11, 9]],
ploidy,
equal_nan=False)
def test_coverage3():
with pytest.raises(ValueError):
with open_bgen(
example_filepath2("example.bgen"),
samples_filepath=example_filepath(
"complex.sample"), # Wrong size sample file
verbose=False,
) as _:
pass
with pytest.raises(ValueError):
with open_bgen(
example_filepath2("complex.bgen"),
verbose=False,
) as _:
pass
def test_read_indexing():
filepath = example_filepath2("example.32bits.bgen")
bgen2 = open_bgen(filepath, verbose=False)
full = bgen2.read()
val = bgen2.read(22)
assert np.allclose(full[:, [22]], val, equal_nan=True)
val = bgen2.read([22])
assert np.allclose(full[:, [22]], val, equal_nan=True)
val = bgen2.read([22, 30])
assert np.allclose(full[:, [22, 30]], val, equal_nan=True)
val = bgen2.read(slice(10, 30, 2))
assert np.allclose(full[:, 10:30:2], val, equal_nan=True)
bool_list = [i % 2 == 0 for i in range(bgen2.nvariants)]
val = bgen2.read(bool_list)
assert np.allclose(full[:, bool_list], val, equal_nan=True)
val = bgen2.read((None, None))
assert np.allclose(full, val, equal_nan=True)
val = bgen2.read((22, None))
assert np.allclose(full[[22], :], val, equal_nan=True)
val = bgen2.read((22, [11, 9]))
assert np.allclose(full[[22], :][:, [11, 9]], val, equal_nan=True)
val = bgen2.read(([22, 30], [11, 9]))
assert np.allclose(full[[22, 30], :][:, [11, 9]], val, equal_nan=True)
val = bgen2.read((slice(10, 30, 2), [11, 9]))
assert np.allclose(full[10:30:2, :][:, [11, 9]], val, equal_nan=True)
bool_list = [i % 2 == 0 for i in range(bgen2.nsamples)]
val = bgen2.read((bool_list, [11, 9]))
assert np.allclose(full[bool_list, :][:, [11, 9]], val, equal_nan=True)
val = bgen2.read(([-1], [-1]))
assert np.allclose(full[-1, -1], val, equal_nan=True)
val = bgen2.read(np.s_[10:30:2, :5])
assert np.allclose(full[10:30:2, :5, :], val, equal_nan=True)
# Read no variants
val, missing, ploidy = bgen2.read([], return_missings=True, return_ploidies=True)
assert val.shape == (bgen2.nsamples, 0, bgen2.max_combinations)
assert missing.shape == (bgen2.nsamples, 0)
assert ploidy.shape == (bgen2.nsamples, 0)
# Read no samples and no variants
val, missing, ploidy = bgen2.read(
([], []), return_missings=True, return_ploidies=True
)
assert val.shape == (0, 0, bgen2.max_combinations)
assert missing.shape == (0, 0)
assert ploidy.shape == (0, 0)
def test_bgen_samples_specify_samples_file():
data = open_bgen(
example_filepath2("complex.23bits.bgen"),
samples_filepath=example_filepath("complex.sample"),
verbose=False,
)
samples = ["sample_0", "sample_1", "sample_2", "sample_3"]
assert all(data.samples == samples)
def test_freq():
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen:
variant_index = bgen.rsids == "RSID_6"
e = bgen.allele_expectation(variant_index)
f = bgen.allele_frequency(e)
assert_allclose(f[0, 0], 229.23103218810434)
assert_allclose(f[0, 1], 270.7689678118956)
def test_bgen_samples_not_present():
with open_bgen(
example_filepath2("complex.23bits.no.samples.bgen"),
allow_complex=True,
verbose=False,
) as data:
samples = ["sample_0", "sample_1", "sample_2", "sample_3"]
assert all(data.samples == samples)
def test_coverage4(tmp_path):
oldpwd = os.getcwd()
filepath = example_filepath2("example.32bits.bgen")
try:
os.chdir(filepath.parent)
with open_bgen(filepath.name) as bgen2:
assert bgen2.shape == (500, 199, 3)
finally:
os.chdir(oldpwd)
def filtered_microarray_snps(region):
"""
Iterate over a region returning genotypes at SNP loci.
Returns microarray measured SNPs that have been QCed and phased
(i.e. the ones in the bgen files) which does not include
all microarray measured SNPs
Yields tuples
(genotypes, chrom, pos, alleles, locus_filtered)
currently, locus_filtered is always None
genotypes are pairs of indicators:
0: 1st allele
1: 2nd allele
note that bgen files don't distinguish between reference and alt
alleles. 1st allele may or may not be the reference. (This
is different than imputed SNPs!)
Expecting all samples in the input file to have 0 or 1 probs
so not filtering any calls
No filtering for samples with rare genotypes
Loci with only single genotypes remaining are returned - it is up to
calling code to filter these out
"""
chrom, posses = region.split(':')
start, end = posses.split('-')
start = int(start)
end = int(end)
bgen_fname = f'{ukb}/microarray/ukb_hap_chr{chrom}_v2.bgen'
bgen = bgen_reader.open_bgen(bgen_fname, allow_complex=True, verbose=False)
for variant_num, pos in enumerate(bgen.positions):
if pos < start:
continue
if pos > end:
break
probs, missing, ploidy = bgen.read(variant_num,
return_missings=True,
return_ploidies=True)
# make sure the record looks as expected
assert np.all(np.logical_or(probs == 0, probs == 1))
assert probs.shape[2] == 4
assert bgen.phased[variant_num]
assert np.all(ploidy == 2)
assert not np.any(missing)
# Since all alleles are bialleleic, the genotype can
# be written as the presence or absence of the second allele
# for each haplotype for each participant
reformatted_gts = probs[:, 0, [1, 3]]
yield (reformatted_gts, chrom, pos, bgen.allele_ids[variant_num], None,
None)
def test_threads():
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
for num_threads in [1, 2]:
for slice in [np.s_[:, :], np.s_[:, []]]:
val = bgen2.read(index=slice, num_threads=num_threads)
row_count = len(bgen2.samples[slice[0]])
col_count = len(bgen2.ids[slice[1]])
assert val.shape == (row_count, col_count, 3)
def run(path, batch_size=1000):
ct = 0
with open_bgen(path) as bgen:
n = bgen.nvariants
print(f'Found {n} variants')
for i in range(0, n, batch_size):
val = bgen.read(slice(i, i + batch_size))
ct += val.shape[0] * val.shape[1]
print(f'Number of entries read: {ct}')
def test_bgen_samples_specify_samples_file():
with open_bgen(
example_filepath2("complex.23bits.bgen"),
samples_filepath=example_filepath("complex.sample"),
allow_complex=True,
verbose=False,
) as data:
samples = ["sample_0", "sample_1", "sample_2", "sample_3"]
assert all(data.samples == samples)
def test_read_dtype_and_order():
filepath = example_filepath2("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
full = bgen2.read()
assert full.dtype == np.float64
assert full.flags["F_CONTIGUOUS"] and not full.flags["C_CONTIGUOUS"]
val = bgen2.read(None, dtype="float32", order="C")
assert val.dtype == np.float32
assert val.flags["C_CONTIGUOUS"] and not val.flags["F_CONTIGUOUS"]
assert np.allclose(full, val, atol=5e-8, equal_nan=True)
def test_to_improve_coverage():
filepath = example_filepath2("example.32bits.bgen")
bgen2 = open_bgen(filepath, verbose=False) # Creates metadata2.mmm file
assert_equal(bgen2.ncombinations[-1], 3)
assert_equal(bgen2.phased[-1], False)
with open_bgen(filepath) as bgen2: # Reuses metadata2.mmm file
assert_equal(str(bgen2), "open_bgen('{0}')".format(filepath.name))
assert_equal(bgen2.nsamples, 500)
assert_equal(bgen2.nvariants, 199)
assert_equal(bgen2.shape, (500, 199, 3))
assert_equal(bgen2.ids[-1], "SNPID_200")
assert_equal(bgen2.rsids[-1], "RSID_200")
assert_equal(bgen2.chromosomes[-1], "01")
assert_equal(bgen2.positions[-1], 100001)
assert_equal(bgen2.nalleles[-1], 2)
assert_equal(bgen2.allele_ids[-1], "A,G")
assert_equal(bgen2.ncombinations[-1], 3)
assert_equal(bgen2.phased[-1], False)
assert_equal(bgen2.samples[-1], "sample_500")
b = [
0.97970582847010945215516,
0.01947019668749305418287,
0.00082397484239749366197,
]
g = bgen2.read((2, 1))
assert_allclose(g[0, 0, :], b)
g = bgen2.read()
assert_allclose(g[2, 1, :], b)
# confirm that out-of-date metadata2 file will be updated
metadata2 = bgen2._metadata2_path
del bgen2
assert os.path.getmtime(metadata2) >= os.path.getmtime(filepath)
filepath.touch()
assert os.path.getmtime(metadata2) <= os.path.getmtime(filepath)
bgen2 = open_bgen(filepath, verbose=False) # Creates metadata2.mmm file
del bgen2
assert os.path.getmtime(metadata2) >= os.path.getmtime(filepath)
def compute(pgs, bedfile=None, bgenfile=None, par_gts_f=None, ped=None, sib=False, compute_controls=False, verbose=True):
"""Compute a polygenic score (PGS) for the individuals with observed genotypes and observed/imputed parental genotypes.
Args:
par_gts_f : :class:`str`
path to HDF5 file with imputed parental genotypes
gts_f : :class:`str`
path to bed file with observed genotypes
pgs : :class:`snipar.pgs`
the PGS, defined by the weights for a set of SNPs and the alleles of those SNPs
sib : :class:`bool`
Compute the PGS for genotyped individuals with at least one genotyped sibling and observed/imputed parental genotypes. Default False.
compute_controls : :class:`bool`
Compute polygenic scores for control families (families with observed parental genotypes set to missing). Default False.
Returns:
pg : :class:`snipar.gtarray`
Return the polygenic score as a genotype array with columns: individual's PGS, mean of their siblings' PGS, observed/imputed paternal PGS,
observed/imputed maternal PGS
"""
# Check for SNP overlap
if bedfile is not None:
bed = Bed(bedfile, count_A1=True)
snp_ids = bed.sid
if bgenfile is not None:
bgen = open_bgen(bgenfile)
snp_ids = bgen.ids
if np.unique(snp_ids).shape[0] == 1:
snp_ids = bgen.rsids
snp_set = set(snp_ids)
in_snp_set = np.array([x in snp_set for x in pgs.snp_ids])
if np.sum(in_snp_set)==0:
print('No overlap between variants in weights file and observed genotypes')
return None
else:
# Get genotype matrix
G = get_gts_matrix(bedfile=bedfile, bgenfile=bgenfile, par_gts_f=par_gts_f, ped=ped, snp_ids=pgs.snp_ids, sib=sib, compute_controls=compute_controls, verbose=verbose)
if sib:
cols = np.array(['proband', 'sibling', 'paternal', 'maternal'])
else:
cols = np.array(['proband', 'paternal', 'maternal'])
if compute_controls:
pgs_out = [pgs.compute(x,cols) for x in G[0:3]]
if sib:
o_cols = np.array(['proband', 'sibling', 'parental'])
else:
o_cols = np.array(['proband','parental'])
pgs_out.append(pgs.compute(G[3], o_cols))
return pgs_out
else:
return pgs.compute(G,cols)
def test_dosage1():
filepath = example_filepath("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen:
variant_index = 3
e = bgen.allele_expectation(variant_index)
# Compute the dosage when considering the allele
# in position 1 as the reference/alternative one.
alt_allele_index = 1
dosage = e[..., alt_allele_index]
# Print the dosage of the first five samples only.
# print(dosage[:5])
assert_allclose(dosage[:2, 0],
[1.9618530841455453, 0.009826655967586362])
def test_open_bgen_complex():
filepath = example_filepath2("complex.23bits.bgen")
with open_bgen(filepath, allow_complex=True, verbose=False) as bgen2:
assert_equal(bgen2.chromosomes[0], "01")
assert_equal(bgen2.ids[0], "")
assert_equal(bgen2.nalleles[0], 2)
assert_equal(bgen2.allele_ids[0], "A,G")
assert_equal(bgen2.positions[0], 1)
assert_equal(bgen2.rsids[0], "V1")
assert_equal(bgen2.chromosomes[7], "01")
assert_equal(bgen2.ids[7], "")
assert_equal(bgen2.nalleles[7], 7)
assert_equal(bgen2.allele_ids[7], "A,G,GT,GTT,GTTT,GTTTT,GTTTTT")
assert_equal(bgen2.positions[7], 8)
assert_equal(bgen2.rsids[7], "M8")
assert_equal(bgen2.chromosomes[-1], "01")
assert_equal(bgen2.ids[-1], "")
assert_equal(bgen2.nalleles[-1], 2)
assert_equal(bgen2.allele_ids[-1], "A,G")
assert_equal(bgen2.positions[-1], 10)
assert_equal(bgen2.rsids[-1], "M10")
assert_equal(bgen2.samples[0], "sample_0")
assert_equal(bgen2.samples[3], "sample_3")
g = bgen2.read((0, 0))
assert_allclose(g[0, 0, :2], [1, 0])
assert isnan(g[0, 0, 2])
g = bgen2.read((1, 0))
assert_allclose(g[0, 0, :3], [1, 0, 0])
g = bgen2.read((-1, -1))
assert_allclose(g[0, 0, :5], [0, 0, 0, 1, 0])
ploidy = bgen2.read(0,
return_probabilities=False,
return_ploidies=True)
assert_allclose(ploidy[:, 0], [1, 2, 2, 2])
ploidy = bgen2.read(-1,
return_probabilities=False,
return_ploidies=True)
assert_allclose(ploidy[:, 0], [4, 4, 4, 4])
assert_equal(bgen2.phased.dtype.name, "bool")
ideal = array(
[False, True, True, False, True, True, True, True, False, False])
assert array_equal(bgen2.phased, ideal)
def __init__(
self,
filepath: Union[str, Path],
samples_filepath: Optional[Union[str, Path]] = None,
allow_complex: bool = False,
verbose: bool = True,
):
self._bgen = bgen_reader.open_bgen(filepath,
allow_complex=allow_complex,
verbose=verbose)
self._samples = self._read_sample(samples_filepath)
if self._bgen.samples.shape[0] != self._samples.shape[0]:
raise ValueError(
'sample file length and bgen file length do not match.')
def open_bgen(filename: str, verbose: bool = False) -> bgen_reader.open_bgen:
"""Wrapper of bgen_reader.open_bgen that checks if sample ids make sense."""
bgen = bgen_reader.open_bgen(filename, verbose=verbose)
if bgen.samples[0] == 'sample_0':
print(
'WARNING: Sample ids in bgen file are generic. Trying to read the corresponding .sample file ...'
)
samples_filepath = filename[:-4] + 'sample'
if not path.exists(samples_filepath):
raise FileNotFoundError(f'{samples_filepath} does not exist.')
bgen = _bgen(filename,
verbose=verbose,
samples_filepath=samples_filepath)
return bgen
def test_read_max_combinations():
filepath = example_filepath2("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
assert (np.mean(np.isnan(bgen2.read())) < 2.1e-05
) # main data as only a few missing
val = bgen2.read(max_combinations=5)
assert (np.mean(np.isnan(val[:, :, :3])) < 2.1e-05
) # main data as only a few missing
assert np.all(np.isnan(val[:, :, 3:])) # all the extra are NaN
with pytest.raises(ValueError):
bgen2.read(max_combinations=2)
with pytest.raises(ValueError):
bgen2.read(max_combinations=1)
with pytest.raises(ValueError):
bgen2.read(max_combinations=0)
def test_open_bgen_variants_info():
filepath = example_filepath2("example.32bits.bgen")
with open_bgen(filepath, verbose=False) as bgen2:
assert_equal(bgen2.chromosomes[0], "01")
assert_equal(bgen2.ids[0], "SNPID_2")
assert_equal(bgen2.nalleles[0], 2)
assert_equal(bgen2.allele_ids[0], "A,G")
assert_equal(bgen2.positions[0], 2000)
assert_equal(bgen2.rsids[0], "RSID_2")
assert_equal(bgen2.chromosomes[7], "01")
assert_equal(bgen2.ids[7], "SNPID_9")
assert_equal(bgen2.nalleles[7], 2)
assert_equal(bgen2.allele_ids[7], "A,G")
assert_equal(bgen2.positions[7], 9000)
assert_equal(bgen2.rsids[7], "RSID_9")
assert_equal(bgen2.chromosomes[-1], "01")
assert_equal(bgen2.ids[-1], "SNPID_200")
assert_equal(bgen2.nalleles[-1], 2)
assert_equal(bgen2.allele_ids[-1], "A,G")
assert_equal(bgen2.positions[-1], 100001)
assert_equal(bgen2.rsids[-1], "RSID_200")
assert_equal(bgen2.samples[0], "sample_001")
assert_equal(bgen2.samples[7], "sample_008")
assert_equal(bgen2.samples[-1], "sample_500")
g = bgen2.read((0, 0))
assert all(isnan(g[0, 0, :]))
g = bgen2.read((1, 0))
a = [0.027802362811705648, 0.00863673794284387, 0.9635608992454505]
assert_allclose(g[0, 0, :], a)
b = [
0.97970582847010945215516,
0.01947019668749305418287,
0.00082397484239749366197,
]
g = bgen2.read((2, 1))
assert_allclose(g[0, 0, :], b)