com.google.cloud.genomics.dataflow.functions.CalculateTransmissionProbability Maven / Gradle / Ivy

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/*
 * Copyright (C) 2014 Google Inc.
 *
 * Licensed 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 com.google.cloud.genomics.dataflow.functions;

import com.google.cloud.dataflow.sdk.transforms.DoFn;
import com.google.cloud.dataflow.sdk.values.KV;
import com.google.cloud.genomics.dataflow.model.Allele;

/*
 * Calculates the Transmission probability of each Allele.
 *
 * For now, this class only calculates only a simple ratio by dividing the number of observed
 * transmission of a certain allele (i.e. total times this allele is observed in a child) with the
 * total number of occurences of the allele.
 */

public class CalculateTransmissionProbability
    extends DoFn>, KV> {

  @Override
  public void processElement(ProcessContext c) {
    KV> input = c.element();
    double transmitted = 0, total = 0;
    for (Boolean b : input.getValue()) {
      if (b) {
        transmitted += 1;
      }
      total += 1;
    }
    double tp = transmitted / total;
    c.output(KV.of(input.getKey(), tp));
  }
}