#1470 closed enhancement (fixed)

Use multiple threads when loading existing VCF files in the genotype QC wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.46
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

This could save some time when running this wizard.

Change History (3)

comment:1 by Nicklas Nordborg, 12 months ago

In [7071]

Referenes #1470: Use multiple threads when loading existing VCF files in the genotype QC wizard

The VCF files are now parsed by separate threads. Unfortunately we don't gain that much. It seems to be because getting the reference to the actual VCF file requires additional database queries which takes about the same amount of time as the parsing. So the parsing threads will have to wait for the next file and it doesn't help if we have more than 2.

I think it should be possible to improve this if we can get some functionality into the BASE core API for loading AnyToAny links. See https://base.thep.lu.se/ticket/2296

Last edited 12 months ago by Nicklas Nordborg (previous) (diff)

comment:2 by Nicklas Nordborg, 12 months ago

In 7073:

References #1470: Use multiple threads when loading existing VCF files in the genotype QC wizard

Changed the implementation to use the FastLinkLoader API introduced in BASE 3.19.8.

comment:3 by Nicklas Nordborg, 11 months ago

Resolution: fixed
Status: newclosed
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