PCA changes: no longer produces files, new --arrays option

PCA writes to annotations instead of files.

  1. --scores [-s] option is required, defines sa path for the k sample PC scores
  2. --loadings [-l] option is optional, defines va path for variant loadings (if this argument is not passed, pca will be a little faster)
  3. --eigenvalues [-e] option is optional, defines global path for the k eigenvalues

The --arrays option produces Array[Double] for scores and loadings rather Struct{ PC1: Double, PC2: Double, PC3: Double, ...}