Status of new hdf5 storage model.

[BoPeng]

This thread is used to update the implementation of the HDF5 storage model.

Pending

• init:

  • --store added to allow specification of storage model.
  • --parent and --children raise NotImplemented error with --store hdf5

• import:

  • Import vcf files to hdf5 storage is done.
  • import non-vcf files will not be supported. users are asked to use sqlite storage model instead.

• show:

  • show table works
  • PENDING show genotypes not working for hdf5.

• update

  • There are sqlite extensions

• select

• exclude

• output

  • There are sqlite extensions

• export

• remove

  • remove variants is difficult to port
  • remove genotype is difficult to port

• associate

• admin

  • merge-samples is difficult to port

Completed

• liftover: liftover does not involve genotype storage
• use: use does not involve genotype storage
• compare: compare does not involve genotype storage
• execute: SQL query can only be applied to sqlite storage.
• phenotype: phenotype does not involve genotype storage