[ADAM-1964] Lower point where phred conversions are done using log code.

Resolves bigdatagenomics#1964. There was an underflow somewhere causing round trip from
log space values to Phred to mismatch for values between 164 and 254.
This change lowers the point where we switch from using the precomputed
table to where we use the log math. Also, we add a unit test checking
round trip values using PhredUtils.

adam-core/src/main/scala/org/bdgenomics/adam/util/PhredUtils.scala

@@ -55,7 +55,7 @@ object PhredUtils extends Serializable {
    * @return The input phred score as a log success probability.
    */
   def phredToLogProbability(phred: Int): Double = {
-    if (phred < 255) {
+    if (phred < 156) {
       log(phredToSuccessProbability(phred)).toFloat
     } else {
       log1p(-exp(phred * MLOG10_DIV10))

adam-core/src/test/scala/org/bdgenomics/adam/util/PhredUtilsSuite.scala

@@ -43,4 +43,21 @@ class PhredUtilsSuite extends FunSuite {
     val phred = PhredUtils.logProbabilityToPhred(-0.0)
     assert(phred === 3233)
   }
+
+  test("round trip log probabilities") {
+    def roundTrip(i: Int): Int = {
+      PhredUtils.logProbabilityToPhred(PhredUtils.phredToLogProbability(i))
+    }
+
+    (0 to 3228).foreach(i => {
+      assert(i === roundTrip(i))
+    })
+
+    // there is roundoff above 3228 due to floating point underflow
+    assert(3228 === roundTrip(3229))
+    assert(3230 === roundTrip(3230))
+    assert(3230 === roundTrip(3231))
+    assert(3233 === roundTrip(3232))
+    assert(3233 === roundTrip(3233))
+  }
 }