PCA writes to annotations instead of files.
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--scores [-s]option is required, defines sa path for the k sample PC scores -
--loadings [-l]option is optional, defines va path for variant loadings (if this argument is not passed, pca will be a little faster) -
--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, ...}