def run_vcfc_sparse_query(config: Config, filename: str, ref: str, start: int,
end: int) -> float:
if not os.path.exists(filename):
raise RuntimeError('%s does not exist' % filename)
cmd_args = [
config.get_vcfc_release_cmd(), 'sparse-query', filename,
'%s:%d-%d' % (ref, start, end)
]
return time_cmd(cmd_args)
def create_vcfc_sparse_external_index(config: Config, filename: str) -> float:
if not os.path.exists(filename):
raise RuntimeError('%s does not exist' % filename)
cmd_args = [
config.get_vcfc_release_cmd(),
'create-sparse-index',
filename,
# '%s:%d-%d' % (ref, start, end)
]
return time_cmd(cmd_args)
def run_vcfc_binned_index_query(config: Config, filename: str, ref: str,
start: int, end: int) -> float:
if not os.path.exists(filename):
raise RuntimeError('%s does not exist' % filename)
if not os.path.exists(filename + '.vcfci'):
raise RuntimeError('%s does not exist' % (filename + '.vcfci'))
cmd_args = [
config.get_vcfc_release_cmd(), 'query-binned-index', filename,
'%s:%d-%d' % (ref, start, end)
]
return time_cmd(cmd_args)
def create_binned_index(config: Config, filename: str, bin_size: int) -> float:
cmd_args = [
config.get_vcfc_release_cmd(), 'create-binned-index',
str(bin_size), filename
]
return time_cmd(cmd_args)