Understanding the implementation of the StrandOddsRatio

[nh13]

I am trying to understand the calculation of the StrandOddsRatio. The online documentation and javadoc for the StrandOddsRatio class shows it as:

$$ refRatio = \frac{max(X[0][0], X[0][1])}{min(X[0][0], X[0][1} $$

Nonetheless, my reading of the code shows it as

$$ refRatio = \frac{min(X[0][0], X[0][1])}{max(X[0][0], X[0][1} $$

The code is:

final double refRatio = min(t00, t01)/ max(t00, t01);

The docs say its max/min while the code does min/max. The same is true for the docs and implementation of altRatio. It looks like either a bug, or the docs need to be updated.

[nh13]

Related to #5698

[ldgauthier]

That might have been me. I'm a little dyslexic.

[nh13]

No worries.

[sooheelee]

@nh13, the next release should reflect SOR documentation updates from #5703.