bigdatagenomics/adam — pull request #71 by arahuja (2014-01-28 21:04:00+00:00)
Title: Change RecalTable to use optimized phred calculations

Replacing RecalTable phred conversion functions with optimized versions from PhredUtils
1) Should be faster due to caching done in PhredUtils
2) The ones in recal table actually had a bug as well, due to integer division in the exponent.

scala> def qualToErrorProb(q: Byte): Double = math.pow(10.0, -q / 10)
qualToErrorProb: (q: Byte)Double

scala> qualToErrorProb(5)
res0: Double = 1.0

scala> math.pow(10.0, -0.5)
res1: Double = 0.31622776601683794

scala> math.pow(10.0, -5/10)
res2: Double = 1.0