org.broadinstitute.gatk.utils.Utils.getRandomGenerator()方法的使用及代码示例

x33g5p2x  于2022-02-01 转载在 其他  
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本文整理了Java中org.broadinstitute.gatk.utils.Utils.getRandomGenerator()方法的一些代码示例，展示了Utils.getRandomGenerator()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Utils.getRandomGenerator()方法的具体详情如下：
包路径：org.broadinstitute.gatk.utils.Utils
类名称：Utils
方法名：getRandomGenerator

Utils.getRandomGenerator介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Get a random int between min and max (inclusive) using the global GATK random number generator
 *
 * @param min lower bound of the range
 * @param max upper bound of the range
 * @return a random int >= min and <= max
 */
public static int randomIntegerInRange( final int min, final int max ) {
  return Utils.getRandomGenerator().nextInt(max - min + 1) + min;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Create random read qualities
 *
 * @param length the length of the read
 * @return an array with randomized base qualities between 0 and 50
 */
public static byte[] createRandomReadQuals(int length) {
  Random random = Utils.getRandomGenerator();
  byte[] quals = new byte[length];
  for (int i = 0; i < length; i++)
    quals[i] = (byte) random.nextInt(50);
  return quals;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Return a random base index, excluding some base index.
 *
 * @param excludeBaseIndex the base index to exclude
 * @return a random base index, excluding the one specified (A=0, C=1, G=2, T=3)
 */
static public int getRandomBaseIndex(int excludeBaseIndex) {
  int randomBaseIndex = excludeBaseIndex;
  while (randomBaseIndex == excludeBaseIndex) {
    randomBaseIndex = Utils.getRandomGenerator().nextInt(4);
  }
  return randomBaseIndex;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Returns n random indices drawn with replacement from the range 0..(k-1)
 *
 * @param n the total number of indices sampled from
 * @param k the number of random indices to draw (with replacement)
 * @return a list of k random indices ranging from 0 to (n-1) with possible duplicates
 */
static public ArrayList<Integer> sampleIndicesWithReplacement(final int n, final int k) {
  ArrayList<Integer> chosen_balls = new ArrayList<Integer>(k);
  for (int i = 0; i < k; i++) {
    //Integer chosen_ball = balls[rand.nextInt(k)];
    chosen_balls.add(Utils.getRandomGenerator().nextInt(n));
    //balls.remove(chosen_ball);
  }
  return chosen_balls;
}

代码示例来源：origin: broadgsa/gatk-protected

public List<VariantDatum> getRandomDataForPlotting( final int numToAdd, final List<VariantDatum> trainingData, final List<VariantDatum> antiTrainingData, final List<VariantDatum> evaluationData ) {
  final List<VariantDatum> returnData = new ExpandingArrayList<>();
  Collections.shuffle(trainingData, Utils.getRandomGenerator());
  Collections.shuffle(antiTrainingData, Utils.getRandomGenerator());
  Collections.shuffle(evaluationData, Utils.getRandomGenerator());
  returnData.addAll(trainingData.subList(0, Math.min(numToAdd, trainingData.size())));
  returnData.addAll(antiTrainingData.subList(0, Math.min(numToAdd, antiTrainingData.size())));
  returnData.addAll(evaluationData.subList(0, Math.min(numToAdd, evaluationData.size())));
  Collections.shuffle(returnData, Utils.getRandomGenerator());
  return returnData;
}

代码示例来源：origin: broadgsa/gatk

@Override
public void submit( final T newRead ) {
  if ( Utils.getRandomGenerator().nextInt(10000) < cutoffForInclusion || doNotDiscardItem(newRead) ) {
    selectedReads.add(newRead);
  }
  else {
    numDiscardedItems++;
  }
}

代码示例来源：origin: broadgsa/gatk

@BeforeClass
public void init() {
  random = Utils.getRandomGenerator();
}

代码示例来源：origin: broadgsa/gatk-protected

private List<Integer> generateElementCollection(final int elementCount, final int maxElement) {
  final Random rnd = Utils.getRandomGenerator();
  final List<Integer> elementList = new ArrayList<>(elementCount);
  for (int i = 0; i < elementCount; i++)
    elementList.add(rnd.nextInt(maxElement + 1));
  return elementList;
}

代码示例来源：origin: broadgsa/gatk-protected

private Map<Allele,List<Allele>> randomAlleleMap(final Allele[] fromAlleles, final Allele[] toAlleles) {
  final Map<Allele,List<Allele>> result = new HashMap<>(toAlleles.length);
  for (final Allele toAllele : toAlleles )
    result.put(toAllele,new ArrayList<Allele>(fromAlleles.length));
  final ArrayList<Allele> remaining = new ArrayList<>(Arrays.asList(fromAlleles));
  int nextToIndex = 0;
  final Random rnd = Utils.getRandomGenerator();
  for (int i = 0; i < fromAlleles.length; i++) {
    final int fromAlleleIndex = rnd.nextInt(remaining.size());
    result.get(toAlleles[nextToIndex]).add(remaining.remove(fromAlleleIndex));
    nextToIndex = (nextToIndex + 1) % toAlleles.length;
  }
  return result;
}

代码示例来源：origin: broadgsa/gatk

private byte[] getDeterministicRandomData ( int size ) {
    Utils.resetRandomGenerator();
    Random rand = Utils.getRandomGenerator();

    byte[] randomData = new byte[size];
    rand.nextBytes(randomData);

    return randomData;
  }
}

代码示例来源：origin: broadgsa/gatk-protected

private AlleleList<Allele> discardAllelesAtRandom(final AlleleList<Allele> likelihoods, final int discardAlleleCount) {
  final Random rnd = Utils.getRandomGenerator();
  final ArrayList<Allele> subset = new ArrayList<>(AlleleListUtils.asList(likelihoods));
  for (int i = 0; i < discardAlleleCount; i++) {
    subset.remove(rnd.nextInt(subset.size()));
  }
  return new IndexedAlleleList<>(subset);
}

代码示例来源：origin: broadgsa/gatk-protected

private void addBaseErrors(final byte[] readBases, final int phredScaledErrorRate) {
    double errorProbability = QualityUtils.qualToErrorProb((byte)phredScaledErrorRate);

    for (int k=0; k < readBases.length; k++) {
      if (Utils.getRandomGenerator().nextDouble() < errorProbability) {
        // random offset
        int offset = BaseUtils.simpleBaseToBaseIndex(readBases[k]);          //0..3
        offset += (Utils.getRandomGenerator().nextInt(3)+1);  // adds 1,2 or 3
        offset %= 4;
        readBases[k] = BaseUtils.baseIndexToSimpleBase(offset);

      }

    }

  }
}

代码示例来源：origin: broadgsa/gatk-protected

@Test(dataProvider = "capacityData")
public void testCapacity(final int initialCapacity, final int elementCount) {
  final IntMaxHeap heap = new IntMaxHeap(initialCapacity);
  final Random rnd = Utils.getRandomGenerator();
  for (int i = 0; i < elementCount; i++) {
    final int v = rnd.nextInt();
    heap.add(v);
  }
}

代码示例来源：origin: broadgsa/gatk-protected

private double[][][] fillWithRandomLikelihoods(final String[] samples, final Allele[] alleles, final ReadLikelihoods<Allele> result) {
  final Random rnd = Utils.getRandomGenerator();
  final double[][][] likelihoods = new double[samples.length][alleles.length][];
  for (int s = 0; s < likelihoods.length; s++) {
    final ReadLikelihoods.Matrix<Allele> sampleLikelihoods = result.sampleMatrix(s);
    for (int a = 0; a < likelihoods[s].length; a++) {
      likelihoods[s][a] = new double[result.sampleReadCount(s)];
      for (int r = 0; r < likelihoods[s][a].length; r++)
        sampleLikelihoods.set(a,r,likelihoods[s][a][r] = -Math.abs(rnd.nextGaussian()));
    }
  }
  return likelihoods;
}

代码示例来源：origin: broadgsa/gatk

@DataProvider(name = "SimplePositionalDownsamplerTestDataProvider")
public Object[][] createSimplePositionalDownsamplerTestData() {
  Utils.resetRandomGenerator();
  for ( int targetCoverage = 1; targetCoverage <= 10000; targetCoverage *= 10 ) {
    for ( int contigs = 1; contigs <= 2; contigs++ ) {
      for ( int numStacks = 0; numStacks <= 10; numStacks++ ) {
        List<Integer> stackSizes = new ArrayList<Integer>(numStacks);
        for ( int stack = 1; stack <= numStacks; stack++ ) {
          stackSizes.add(Utils.getRandomGenerator().nextInt(targetCoverage * 2) + 1);
        }
        new SimplePositionalDownsamplerTest(targetCoverage, stackSizes, contigs > 1);
      }
    }
  }
  return SimplePositionalDownsamplerTest.getTests(SimplePositionalDownsamplerTest.class);
}

代码示例来源：origin: broadgsa/gatk

private static GenotypesContext createGenotypesContext(final int numGenotypes, final List<Allele> alleles) {
  Utils.resetRandomGenerator();
  final Random random = Utils.getRandomGenerator();
  final GenotypesContext gc = GenotypesContext.create();
  for ( int i = 0; i < numGenotypes; i++ ) {
    // choose alleles at random
    final List<Allele> myAlleles = new ArrayList<Allele>();
    myAlleles.add(alleles.get(random.nextInt(2)));
    myAlleles.add(alleles.get(random.nextInt(2)));
    final Genotype g = new GenotypeBuilder(String.format("%d", i)).alleles(myAlleles).make();
    gc.add(g);
  }
  return gc;
}

代码示例来源：origin: broadgsa/gatk-protected

@Test(dataProvider = "capacityData", dependsOnMethods = {"testEmptynessAndSize"})
public void testClear(final int initialCapacity, final int elementCount) {
  final IntMaxHeap heap = new IntMaxHeap(initialCapacity);
  final Random rnd = Utils.getRandomGenerator();
  for (int i = 0; i < elementCount; i++) {
    final int v = rnd.nextInt();
    heap.add(v);
  }
  heap.clear();
  Assert.assertEquals(heap.size(),0);
  Assert.assertTrue(heap.isEmpty());
}

代码示例来源：origin: broadgsa/gatk

@Test (enabled = true)
public void testGetBasesReverseComplement() {
  int iterations = 1000;
  Random random = Utils.getRandomGenerator();
  while(iterations-- > 0) {
    final int l = random.nextInt(1000);
    GATKSAMRecord read = GATKSAMRecord.createRandomRead(l);
    byte [] original = read.getReadBases();
    byte [] reconverted = new byte[l];
    String revComp = ReadUtils.getBasesReverseComplement(read);
    for (int i=0; i<l; i++) {
      reconverted[l-1-i] = BaseUtils.getComplement((byte) revComp.charAt(i));
    }
    Assert.assertEquals(reconverted, original);
  }
}

代码示例来源：origin: broadgsa/gatk-protected

@Test(dataProvider = "capacityData", dependsOnMethods = {"testCapacity"})
public void testPeek(final int initialCapacity, final int elementCount) {
  final IntMaxHeap heap = new IntMaxHeap(initialCapacity);
  final Random rnd = Utils.getRandomGenerator();
  int top  = rnd.nextInt();
  heap.add(top);
  Assert.assertEquals(heap.peek(),top);
  for (int i = 1; i < elementCount; i++) {
    final int v = rnd.nextInt();
    if (v > top) top = v;
    heap.add(v);
    Assert.assertEquals(heap.peek(),top);
  }
}

代码示例来源：origin: broadgsa/gatk-protected

@Test(dataProvider = "capacityData",dependsOnMethods = {"testCapacity"})
public void testEmptynessAndSize(final int initialCapacity, final int elementCount) {
  final IntMaxHeap heap = new IntMaxHeap(initialCapacity);
  final Random rnd = Utils.getRandomGenerator();
  Assert.assertEquals(heap.size(),0);
  Assert.assertTrue(heap.isEmpty());
  for (int i = 0; i < elementCount; i++) {
    final int v = rnd.nextInt();
    heap.add(v);
    Assert.assertEquals(heap.size(),i+1);
    Assert.assertFalse(heap.isEmpty());
  }
}

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