def wrapper(func, *args, **kwargs):
old_flags = hl._get_flags('cpp')
try:
hl._set_flags(cpp='t')
func(*args, **kwargs)
finally:
hl._set_flags(**old_flags)
def wrapper(func, *args, **kwargs):
prev_flags = {k: v for k, v in hl._get_flags().items() if k in flags}
hl._set_flags(**{k: '1' for k in flags})
try:
return func(*args, **kwargs)
finally:
hl._set_flags(**prev_flags)
def wrapper(func, *args, **kwargs):
flags = hl._get_flags()
prev_lower = flags.get('lower')
prev_lower_only = flags.get('lower_only')
hl._set_flags(lower='1', lower_only='1')
try:
return func(*args, **kwargs)
finally:
hl._set_flags(lower=prev_lower, lower_only=prev_lower_only)
def compile_2k_merge(path):
flagname = 'no_ir_logging'
prev_flag_value = hl._get_flags(flagname).get(flagname)
try:
hl._set_flags(**{flagname: '1'})
vcf = setup(path)
vcfs = [vc_all.transform_gvcf(vcf)] * COMBINE_GVCF_MAX
combined = [vc_all.combine_gvcfs(vcfs)] * 20
with TemporaryDirectory() as tmpdir:
hl.experimental.write_matrix_tables(combined,
os.path.join(
tmpdir,
'combiner-multi-write'),
overwrite=True)
finally:
hl._set_flags(**{flagname: prev_flag_value})
def run(self):
flagname = 'no_ir_logging'
prev_flag_value = hl._get_flags(flagname).get(flagname)
hl._set_flags(**{flagname: '1'})
vds_samples = sum(vds.n_samples for vdses in self.vdses.values()
for vds in vdses)
info(
'Running VDS combiner:\n'
f' VDS arguments: {self._num_vdses} datasets with {vds_samples} samples\n'
f' GVCF arguments: {len(self.gvcfs)} inputs/samples\n'
f' Branch factor: {self.branch_factor}\n'
f' GVCF merge batch size: {self.gvcf_batch_size}')
while not self.finished:
self.save()
self.step()
self.save()
info('Finished VDS combiner!')
hl._set_flags(**{flagname: prev_flag_value})
def wrapper(func, *args, **kwargs):
old_flags = hl._get_flags('cpp')
hl._set_flags(cpp='t')
func(*args, **kwargs)
hl._set_flags(**old_flags)