From d42a1674dcf79792edfb1752a5bb40a4ea8f0964 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Mon, 12 Feb 2024 23:18:24 +0000 Subject: [PATCH] Tweak --- vcf2zarr.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/vcf2zarr.py b/vcf2zarr.py index f9dc03253..7bc0248b5 100644 --- a/vcf2zarr.py +++ b/vcf2zarr.py @@ -27,7 +27,7 @@ def scan(vcfs): @click.argument("vcfs", nargs=-1, required=True) @click.argument("out_path", type=click.Path()) @click.option("-p", "--worker-processes", type=int, default=1) -@click.option("-c", "--column-chunk-size", type=int, default=16) +@click.option("-c", "--column-chunk-size", type=int, default=64) def explode(vcfs, out_path, worker_processes, column_chunk_size): cnv.explode( vcfs, @@ -81,8 +81,9 @@ def to_zarr(columnarised, zarr_path, conversion_spec): @click.command @click.argument("vcfs", nargs=-1, required=True) @click.argument("out_path", type=click.Path()) -def convert(vcfs, out_path): - cnv.convert_vcf(vcfs, out_path, show_progress=True) +@click.option("-p", "--worker-processes", type=int, default=1) +def convert(vcfs, out_path, worker_processes): + cnv.convert_vcf(vcfs, out_path, show_progress=True, worker_processes=worker_processes) @click.command @click.argument("vcfs", nargs=-1, required=True)