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ornl-oxford / genben

Benchmarking of software frameworks, and systems for storage and compute over large-scale genomic data.
MIT License
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[VCF to Zarr] Expose alt_number, chunk_length, and chunk_width as Configuration Options #32

Closed eauel closed 6 years ago

eauel commented 6 years ago

This PR exposes the alt_number, chunk_length, and chunk_width options for VCF to Zarr conversion, which was requested in https://github.com/ornl-oxford/genomics-benchmarks/pull/29#issuecomment-424490953 .

An "auto" option has been added for alt_number in the configuration file. If "auto" is specified, alt_number will be determined/calculated during the VCF to Zarr conversion process, which is what was done previously. If a number is specified, it skips this step and simply uses the provided alt number.

A "default" option has been added for chunk_length and chunk_width in the configuration file. If "default" is specified, the default value from scikit-allel is used.

Two new functions, isint() and isfloat() have been added to config.py to cleanup the code in a few places (removed redundancy).

This PR resolves #31.

alimanfoo commented 6 years ago

Great, thanks @eauel.

eauel commented 6 years ago

Thanks for the feedback @alimanfoo , I have made the requested changes. I also went ahead and raised errors for incorrect values for blosc_compression_level and blosc_shuffle_mode.

alimanfoo commented 6 years ago

Thanks, looks good.

On Mon, 15 Oct 2018, 16:40 Eric Auel, notifications@github.com wrote:

Thanks for the feedback @alimanfoo https://github.com/alimanfoo , I have made the requested changes. I also went ahead and raised errors for incorrect values for blosc_compression_level and blosc_shuffle_mode.

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