• Reduction in memory usage for LD computation when dosages are present;
  • compute LD matrix block-wise rather than all at once
  • expected memory usage is (3NB+ M^2)*8 bytes where N is sample size, B is block size and M is number of variants in LD matrix
  • we recommend using blocks of sizes 1000 as choosing too small block size will increase the number of block pairs evaluated
• Minor bug fixes for LD computation;
• Bug fix for carriage return in optional files
  • in keep/remove/extract/exclude/mask-definition/annotation files