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Test code to create expanded tables for genotype fields.#450

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bw2 wants to merge 6 commits into
arq5x:masterfrom
bw2:genotype_tables
Open

Test code to create expanded tables for genotype fields.#450
bw2 wants to merge 6 commits into
arq5x:masterfrom
bw2:genotype_tables

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@bw2

@bw2 bw2 commented Apr 24, 2015

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Hi guys, here's the code I was using to test query runtimes with expanded-out genotype tables.

Still needs code:

  • to add family-based indexes (pending figuring out sample ids) based on ped
  • allele balance table

@brentp

brentp commented Apr 24, 2015

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that's a nice implementation!
are you then doing the joins in the gemini query -q string?

it will be good to chat about this stuff to figure out how to proceed once we understand the tradeoff of the various approaches.

@bw2

bw2 commented Apr 27, 2015

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Thanks!
For now I was just doing queries and joins in a SQLite shell.

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2 participants