How does one "optionally" use a small amount of RAM?

arshajii / lava

LAVA: Lightweight Assignment of Variant Alleles

lava.csail.mit.edu

MIT License

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How does one "optionally" use a small amount of RAM? #2

Closed alanhoyle closed 7 years ago

alanhoyle commented 7 years ago

ON the main LAVA page, it says, "optionally using as little as 5.2 GB of RAM." How do I make it use less RAM?

arshajii commented 7 years ago

The two things you can do are:

Filter the reference dictionary using lava filt. Just make sure to set GEN_FLT_DATA to 1 before generating the dictionaries.
Use a compact pileup table by setting PCOMPACT to 1.

The constants are all defined in include/lava.h. Let me know if you run into any issues. Also note that the RAM usage will be dependent on the size of your SNP list; that 5.2 GB number is based on the SNP list from the Affymetrix SNP array.