Skip to content

Commit

Permalink
Lint
Browse files Browse the repository at this point in the history
  • Loading branch information
nalinigans committed Dec 27, 2024
1 parent 3d93a58 commit e8a7b02
Showing 1 changed file with 5 additions and 6 deletions.
11 changes: 5 additions & 6 deletions examples/genomicsdb_query
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ import multiprocessing
import os
import re
import sys
from typing import NamedTuple, List
from typing import List, NamedTuple

import genomicsdb_common
import pyarrow as pa
Expand All @@ -55,7 +55,7 @@ def parse_callset_json(callset_file):
callset = json.loads(genomicsdb.read_entire_file(callset_file))
callsets = callset["callsets"]
samples = [callset if isinstance(callset, str) else callset["sample_name"] for callset in callsets]
< return samples
return samples


def parse_callset_json_for_row_ranges(callset_file, samples=None):
Expand Down Expand Up @@ -338,10 +338,11 @@ class OutputConfig(NamedTuple):
json_type: str | None
max_arrow_bytes: int


class Config(NamedTuple):
export_config: GenomicsDBExportConfig
query_config: GenomicsDBQueryConfig
output_config:OutputConfig
output_config: OutputConfig


def configure_export(config: GenomicsDBExportConfig):
Expand Down Expand Up @@ -469,11 +470,9 @@ def main():
if len(configs) == 1:
process(configs[0])
else:
nprocs = min(len(configs), args.nproc)
with multiprocessing.Pool(processes=args.nproc) as pool:
with multiprocessing.Pool(processes=min(len(configs), args.nproc)) as pool:
pool.map(process, configs)


print(f"genomicsdb_query for workspace({workspace}) and intervals({intervals}) completed successfully")


Expand Down

0 comments on commit e8a7b02

Please sign in to comment.