def should_not_depend_on_chunksize(bintable):
# try different chunk sizes
reader = cooler.io.HDF5Aggregator(mock_reads,
chromsizes,
bintable,
chunksize=66)
cooler.io.create(testfile_path, chromsizes, bintable, reader)
with h5py.File(testfile_path, 'r') as h5:
oc1 = h5['indexes']['chrom_offset'][:]
ob1 = h5['indexes']['bin1_offset'][:]
p1 = cooler.pixels(h5, join=False)
reader = cooler.io.HDF5Aggregator(mock_reads,
chromsizes,
bintable,
chunksize=666)
cooler.io.create(testfile_path, chromsizes, bintable, reader)
with h5py.File(testfile_path, 'r') as h5:
oc2 = h5['indexes']['chrom_offset'][:]
ob2 = h5['indexes']['bin1_offset'][:]
p2 = cooler.pixels(h5, join=False)
assert np.all(oc1 == oc2)
assert np.all(ob1 == ob2)
assert np.all(p1.values == p2.values)
def should_work_with_int32_cols(bintable):
# int64
reader = cooler.io.HDF5Aggregator(mock_reads,
chromsizes,
bintable,
chunksize=66)
cooler.io.create(testfile_path, chromsizes, bintable, reader)
with h5py.File(testfile_path, 'r') as h5:
oc1 = h5['indexes']['chrom_offset'][:]
ob1 = h5['indexes']['bin1_offset'][:]
p1 = cooler.pixels(h5, join=False)
# int32
mock_reads32 = MockReads({
'chrms1': mock_reads['chrms1'].astype(np.int32),
'cuts1': mock_reads['cuts1'].astype(np.int32),
'chrms2': mock_reads['chrms2'].astype(np.int32),
'cuts2': mock_reads['cuts2'].astype(np.int32),
})
reader = cooler.io.HDF5Aggregator(mock_reads32,
chromsizes,
bintable,
chunksize=66)
cooler.io.create(testfile_path, chromsizes, bintable, reader)
with h5py.File(testfile_path, 'r') as h5:
oc2 = h5['indexes']['chrom_offset'][:]
ob2 = h5['indexes']['bin1_offset'][:]
p2 = cooler.pixels(h5, join=False)
assert np.all(oc1 == oc2)
assert np.all(ob1 == ob2)
assert np.all(p1.values == p2.values)
