use crossprod when applicable and implement fastSave in step1

weizhou0 / qtl

GNU General Public License v3.0

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Closed mkanai closed 3 months ago

mkanai commented 3 months ago

This PR applies the following:

use crossprod(X, Y) to replace t(X) %*% Y. This reduces the step 1 computation time by 30-50% depending on data sets.
use fastSave::save.pigz for faster save if pigz is available. The output .rda is compatible with standard save
Minor: fix a bug when isphenoFileLarge