arshajii/lava

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

alanhoyle opened this issue · 1 comments

alanhoyle commented

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

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.