[AVOCADO-215] Improve test coverage for org.bdgenomics.avocado.util.L…

…ogPhred.

Resolves bigdatagenomics#215. Adds test suite and removes unused success probability method.

avocado-core/src/main/scala/org/bdgenomics/avocado/util/LogPhred.scala

@@ -23,27 +23,6 @@ object LogPhred {
 
   private val LOG10 = mathLog(10.0)
 
-  /**
-   * Conversion between log _success_ probabilities and Phred scores.
-   *
-   * Q = -10 log_{10} (1 - p)
-   *
-   * If l = ln p, then:
-   *
-   * l_e = ln 1 + ln (1 - exp(l_e / 1))
-   *     = ln(1 - exp(l_e))
-   * Q = -10 l_e / ln 10
-   *
-   * @note Just remember kids: if you want to live a happy, fulfilling life, don't use Phred!
-   * @note We don't have a conversion the other way around because it doesn't really make sense.
-   *
-   * @param l Log probability.
-   * @return Returns the Phred score corresponding to that log probability.
-   */
-  def logSuccessToPhred(l: Double): Double = {
-    (-10.0 * mathLog(-expm1(l)) / LOG10)
-  }
-
   /**
    * Conversion between log _error_ probabilities and Phred scores.
    *

avocado-core/src/test/scala/org/bdgenomics/avocado/util/LogPhredSuite.scala

@@ -0,0 +1,31 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.avocado.util
+
+import org.scalatest.FunSuite
+import scala.math.log
+
+class LogPhredSuite extends FunSuite {
+
+  test("convert log error probabilities to phred scores") {
+    val phred10 = LogPhred.logErrorToPhred(log(0.1))
+    assert(phred10 > 9.999 && phred10 < 10.001)
+    val phred50 = LogPhred.logErrorToPhred(log(0.00001))
+    assert(phred50 > 49.999 && phred50 < 50.001)
+  }
+}