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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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vtools remove variants does not work for hdf5 #45

Open BoPeng opened 7 years ago

BoPeng commented 7 years ago

The syntax is vtools remove variants TABLE where TABLE is a variant table. In sqlite, the implementation is something like (code]

DELETE FROM genotype_2 WHERE variant_id IN (SELECT variant_id from TABLE)

Not sure what API to use though because all the IDs should be passed to HDF5.

jma7 commented 7 years ago

It seems the remove of variants, samples and genotypes are not reversible? Is this the ideal way? How about use a column to mark the visibility?

BoPeng commented 7 years ago

It is certainly ok as long as that does not affect the performance of retrieving genotype (variant) etc.