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Support loading a subset of VCF fields #1670

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fnothaft opened this Issue Aug 18, 2017 · 0 comments

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fnothaft commented Aug 18, 2017

Parsing all admissible VCF fields may be more expensive than is warranted for all uses. We should allow users to project a set of VCF fields on load.

@fnothaft fnothaft self-assigned this Aug 18, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Aug 18, 2017

[ADAM-1670] Add ability to selectively project VCF fields.
Resolves bigdatagenomics#1670. Adds a method loadVcfWithProjection to ADAMContext. This method
takes a list of INFO/FORMAT field names, which are then applied as filters to
the set of header lines used when creating the VariantContextConverter.

heuermh added a commit that referenced this issue Oct 18, 2017

[ADAM-1670] Add ability to selectively project VCF fields.
Resolves #1670. Adds a method loadVcfWithProjection to ADAMContext. This method
takes a list of INFO/FORMAT field names, which are then applied as filters to
the set of header lines used when creating the VariantContextConverter.

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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