--- a
+++ b/third_party/nucleus/util/math.cc
@@ -0,0 +1,100 @@
+/*
+ * Copyright 2018 Google LLC.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * 3. Neither the name of the copyright holder nor the names of its
+ *    contributors may be used to endorse or promote products derived from this
+ *    software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+
+#include <algorithm>
+#include <cmath>
+
+#include "absl/log/check.h"
+#include "third_party/nucleus/util/math.h"
+
+namespace nucleus {
+
+double PhredToPError(const int phred) {
+  CHECK_GE(phred, 0);
+  return std::pow(10.0, -static_cast<double>(phred) / 10.0);
+}
+
+double PhredToLog10PError(const int phred) {
+  CHECK_GE(phred, 0);
+  return -static_cast<double>(phred) / 10;
+}
+
+double PErrorToPhred(const double perror) {
+  CHECK_GT(perror, 0);
+  CHECK_LE(perror, 1);
+  return Log10PErrorToPhred(PErrorToLog10PError(perror));
+}
+
+int PErrorToRoundedPhred(const double perror) {
+  CHECK_GT(perror, 0);
+  CHECK_LE(perror, 1);
+  return Log10PErrorToRoundedPhred(PErrorToLog10PError(perror));
+}
+
+double PErrorToLog10PError(const double perror) {
+  CHECK_GT(perror, 0);
+  CHECK_LE(perror, 1);
+  return std::log10(perror);
+}
+
+double Log10PErrorToPhred(const double log10_perror) {
+  CHECK_LE(log10_perror, 0);
+  return -10 * log10_perror;
+}
+
+int Log10PErrorToRoundedPhred(const double log10_perror) {
+  return std::abs(std::round(Log10PErrorToPhred(log10_perror)));
+}
+
+double Log10PTrueToPhred(const double log10_ptrue,
+                         const double value_if_not_finite) {
+  const double ptrue = Log10ToReal(log10_ptrue);
+  const double perror = std::log10(1 - ptrue);
+  return std::isfinite(perror) ? -10 * perror : value_if_not_finite;
+}
+
+double Log10ToReal(const double log10_probability) {
+  CHECK_LE(log10_probability, 0.0);
+  return std::pow(10, log10_probability);
+}
+
+std::vector<double> ZeroShiftLikelihoods(
+    const std::vector<double>& likelihoods) {
+  std::vector<double> normalized(likelihoods.size());
+  double max = *std::max_element(likelihoods.cbegin(), likelihoods.cend());
+  std::transform(likelihoods.cbegin(), likelihoods.cend(),
+                 normalized.begin(),
+                 [max](double x) { return x - max; });
+  return normalized;
+}
+
+}  // namespace nucleus