<commit_before>/*
 * 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.model;

import java.util.BitSet;

/**
 * A small container to store variant data needed to compute LD.
 */
public class LdVariant implements java.io.Serializable {
  public enum Genotype {
    UNKNOWN, ZERO, ONE
  }

  private final LdVariantInfo info;

  private final BitSet oneGenotypes;
  private final BitSet missingGenotypes;

  private final int genotypesCount;

  public LdVariant(LdVariantInfo info, Genotype[] genotypes) {
    this.info = info;

    this.oneGenotypes = new BitSet();
    this.missingGenotypes = new BitSet();

    this.genotypesCount = genotypes.length;

    for (int i = 0; i < genotypes.length; i++) {
      if (genotypes[i] == Genotype.ONE) {<commit_msg>Cleanup.<commit_after>/*
 * 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.model;

import java.util.BitSet;

/**
 * A small container to store variant data needed to compute LD.
 */
public class LdVariant implements java.io.Serializable {
  /**
   * Indicates allele for each chromosome. For multiallelic sites, two alleles should be selected
   * for comparison and marked as ZERO or ONE, with reference as ZERO if it is one of the two
   * alleles. The remaining alleles should be marked as UNKNOWN.
   */
  public enum Genotype {
    UNKNOWN, ZERO, ONE
  }

  private final LdVariantInfo info;

  private final BitSet oneGenotypes;
  private final BitSet missingGenotypes;

  private final int genotypesCount;

  public LdVariant(LdVariantInfo info, Genotype[] genotypes) {
    this.info = info;

    this.oneGenotypes = new BitSet();
    this.missingGenotypes = new BitSet();

    this.genotypesCount = genotypes.length;

    for (int i = 0; i < genotypes.length; i++) {
      if (genotypes[i] == Genotype.ONE) {
{'fraction_non_alphanumeric': 0.08202323991797676, 'fraction_numerical': 0.006151742993848257, 'mean_word_length': 3.6832, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4671070', 'n_tokens_mistral': 857, 'n_tokens_neox': 789, 'n_words': 343}