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Minor refactor #194

Merged
merged 5 commits into from Jul 14, 2022
Merged

Minor refactor #194

merged 5 commits into from Jul 14, 2022

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pdiakumis
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A bit of code cleanup/refactor.

  • using python's native os.remove and os.rename for glob cleanup
  • using config_options (instead of parts of arg_dict) throughout the main script
  • creating output directory if it doesn't already exist (does not error out now).
  • keep decompressed VCF only if vcf2maf option is specified (regardless if debug is specified or not)

@pdiakumis pdiakumis marked this pull request as ready for review July 14, 2022 16:23
@sigven sigven merged commit 37dca2c into master Jul 14, 2022
@pdiakumis pdiakumis deleted the patch1 branch July 16, 2022 15:13
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@pdiakumis @sigven