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Fixup code #42

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Merged
merged 1 commit into from
Feb 26, 2024
Merged

Fixup code #42

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13 changes: 5 additions & 8 deletions validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,7 @@
import pathlib
import click

import bio2zarr as bz

# tmp, come up with better names and flatten hierarchy
from bio2zarr import vcf


Expand All @@ -15,7 +13,6 @@
@click.option("-p", "--worker-processes", type=int, default=1)
@click.option("-f", "--force", is_flag=True, default=False)
def cli(vcfs, worker_processes, force):

data_path = pathlib.Path("validation-data")
if len(vcfs) == 0:
vcfs = list(data_path.glob("*.vcf.gz")) + list(data_path.glob("*.bcf"))
Expand All @@ -27,23 +24,23 @@ def cli(vcfs, worker_processes, force):
print(f)
exploded = tmp_path / (f.name + ".exploded")
if force or not exploded.exists():
bz.explode_vcf(
vcf.explode(
[f],
exploded,
worker_processes=worker_processes,
show_progress=True,
)
spec = tmp_path / (f.name + ".spec")
spec = tmp_path / (f.name + ".schema")
if force or not spec.exists():
with open(spec, "w") as specfile:
vcf.generate_spec(exploded, specfile)
vcf.mkschema(exploded, specfile)

zarr = tmp_path / (f.name + ".zarr")
if force or not zarr.exists():
vcf.to_zarr(
vcf.encode(
exploded,
zarr,
conversion_spec=spec,
spec,
worker_processes=worker_processes,
show_progress=True,
)
Expand Down