choishingwan/PRSice: New Compilation and Unit Testing

Update Log

• Implement unit testing for command parsing module
  • command parsing should now be more consistent and should be less likely to be source of bugs
• Now allow the use of --a1 and --a2 instead of --A1 and --A2 to save one shift click
• Can now properly handle bgen file with phasing information
• Re-implement code for covariate parsing. --cov-factor and --cov-col should now have a more well defined behaviour
• --full-back no longer require argument (the expected behaviour)
• Fixed the default distance for --clump-kb, default was Mb instead of Kb (only affects version 2.2.12)
• Correctly capture negative value in --binary-target
• Correctly capture out of bound p-values and other parameters
• Use of --memory will no longer error out PRSice unexpectedly
• Behaviour change for --keep-ambig: Previously, when --keep-ambig was set, PRSice will keep all ambiguous SNP and will not perform any form of flipping, e.g. strand flipping A/C to T/G or dosage flipping A/C to C/A. Now when --keep-ambig was set, PRSice will perform dosage flipping but NOT strand flipping i.e. Base = A/T, Target = T/A, change Target dosage from 0,1,2 for T to 0,1,2 for A. You should only really use --keep-ambig if you are certain that the strand information between your base and target data are identical