本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.createRandomRead()方法的一些代码示例，展示了GATKSAMRecord.createRandomRead()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。GATKSAMRecord.createRandomRead()方法的具体详情如下：
包路径：org.broadinstitute.gatk.utils.sam.GATKSAMRecord
类名称：GATKSAMRecord
方法名：createRandomRead

GATKSAMRecord.createRandomRead介绍

暂无

代码示例

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
public void testExcessAlternativeAllelesKeepRef(){
  // prep data
  final Allele ref = Allele.create("A", true);
  final Allele altC = Allele.create("C", false);
  final Allele altG = Allele.create("G", false);
  final Allele altT = Allele.create("T", false);
  final AlleleList<Allele> indexedAlleleList = new IndexedAlleleList<>(altC, altG, altT, ref);// specifically make the ref allele not at index 0
  final IndexedSampleList indexedSampleList = new IndexedSampleList("Dummy");
  final List<GATKSAMRecord> reads = new ArrayList<>();
  for (int i=0; i<10; ++i) {
    reads.add(GATKSAMRecord.createRandomRead(101));
  }
  final Map<String, List<GATKSAMRecord>> sampleToReads = Collections.singletonMap(indexedSampleList.sampleAt(0), reads);
  final ReadLikelihoods<Allele> readLikelihoods = new ReadLikelihoods<>(indexedSampleList, indexedAlleleList, sampleToReads);
  final PloidyModel ploidyModel = new HomogeneousPloidyModel(indexedSampleList, 2);
  final GenotypingModel genotypingModel = new InfiniteRandomMatingPopulationModel();
  final GenotypingLikelihoods<Allele> genotypeLikelihoods = genotypingModel.calculateLikelihoods(readLikelihoods, new GenotypingData<>(ploidyModel, readLikelihoods));
  // test
  final Set<Allele> excessAltAlleles = HaplotypeCallerGenotypingEngine.excessAlternativeAlleles(genotypeLikelihoods, 2);
  Assert.assertFalse(excessAltAlleles.contains(ref));
  Assert.assertEquals(excessAltAlleles.size(), 1);
}