[benchmark] fix combiner benchmarks #13956
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ehigham
commented
Oct 31, 2023
| from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter | ||
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| from .run import cli as run | ||
| from . import compare, create_resources, combine, summarize, visualize | ||
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| def main(): | ||
| def main(argv=sys.argv[1:]): |
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This change makes it easier for me to launch the benchmark suite in a debugger and change which benchmark i want to debug from within the debugger.
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Hi Chris, would you mind taking a look when you get a chance? I believe you might know the most about the functionality these are exercising. Do the new implementations look ok? Are they benchmarking equivalent functionality? |
chrisvittal
approved these changes
Oct 31, 2023
chrisvittal
requested changes
Oct 31, 2023
Comment on lines
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| def full_combiner_chr22(*paths): | ||
| with TemporaryDirectory() as tmpdir: | ||
| vc_all.run_combiner(list(paths), | ||
| out_file=tmpdir, | ||
| tmp_path='/tmp', | ||
| branch_factor=16, | ||
| reference_genome='GRCh38', | ||
| overwrite=True, | ||
| use_exome_default_intervals=True) | ||
| combiner = new_combiner( | ||
| gvcf_paths=list(paths), | ||
| output_path=tmpdir, | ||
| temp_path='/tmp', | ||
| branch_factor=16, | ||
| reference_genome='GRCh38', | ||
| use_exome_default_intervals=True | ||
| ) | ||
| combiner.run() |
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I believe this is now redundant. This and vds_combiner_chr22 are nearly equivalent.
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Great! I'll remove it. Thanks.
chrisvittal
approved these changes
Nov 2, 2023
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The combiner benchmarks broke following the deletion of the
experimental.vcf_combinerpython package. Re-implement them in terms of thevdspackage.