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choishingwan/PRSice: New Compilation and Unit Testing

Shing Wan Choi; Paul F O'Reilly; monsanto-pinheiro; wenjiany; Vinícius de Souza

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
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