本文整理了Java中org.broadinstitute.gatk.utils.Utils类的一些代码示例，展示了Utils类的具体用法。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类的具体详情如下：
包路径：org.broadinstitute.gatk.utils.Utils
类名称：Utils

Utils介绍

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代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * join an array of strings given a seperator
 * @param separator the string to insert between each array element
 * @param strings the array of strings
 * @return a string, which is the joining of all array values with the separator
 */
public static String join(String separator, String[] strings) {
  return join(separator, strings, 0, strings.length);
}

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

PairHMMTestData(String ref, String nextRef, String read, final byte qual) {
  this.ref = ref;
  this.nextRef = nextRef;
  this.read = read;
  this.baseQuals = this.insQuals = this.delQuals =  Utils.dupBytes(qual, read.length());
  this.gcp =  Utils.dupBytes((byte)10, read.length());
  this.log10l = -1;
  this.newRead = true;
}

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

public String toString() {
    StringBuilder s = new StringBuilder();
    s.append(Utils.dupString('-', 80) + "\n");
    s.append(String.format("Number of examined reads              %d%n", nTotalReads));
    s.append(String.format("Number of clipped reads               %d%n", nClippedReads));
    s.append(String.format("Percent of clipped reads              %.2f%n", (100.0 * nClippedReads) / nTotalReads));
    s.append(String.format("Number of examined bases              %d%n", nTotalBases));
    s.append(String.format("Number of clipped bases               %d%n", nClippedBases));
    s.append(String.format("Percent of clipped bases              %.2f%n", (100.0 * nClippedBases) / nTotalBases));
    s.append(String.format("Number of quality-score clipped bases %d%n", nQClippedBases));
    s.append(String.format("Number of range clipped bases         %d%n", nRangeClippedBases));
    s.append(String.format("Number of sequence clipped bases      %d%n", nSeqClippedBases));
    for (Map.Entry<String, Long> elt : seqClipCounts.entrySet()) {
      s.append(String.format("  %8d clip sites matching %s%n", elt.getValue(), elt.getKey()));
    }
    s.append(Utils.dupString('-', 80) + "\n");
    return s.toString();
  }
}

代码示例来源：origin: broadgsa/gatk

String[] command = Utils.escapeExpressions(args);
  final String cmdline = Utils.join(" ",command);
  System.out.println(String.format("[%s] Executing test %s:%s with GATK arguments: %s", now, testClassName, testName, cmdline));

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

@DataProvider(name = "GetBasesData")
public Object[][] makeGetBasesData() {
  List<Object[]> tests = new ArrayList<>();
  final List<String> frags = Arrays.asList("ACT", "GAC", "CAT");
  for ( int n = 1; n <= frags.size(); n++ ) {
    for ( final List<String> comb : Utils.makePermutations(frags, n, false) ) {
      tests.add(new Object[]{comb});
    }
  }
  return tests.toArray(new Object[][]{});
}

代码示例来源：origin: broadgsa/gatk

/**
 * Splits expressions in command args by spaces and returns the array of expressions.
 * Expressions may use single or double quotes to group any individual expression, but not both.
 * @param args Arguments to parse.
 * @return Parsed expressions.
 */
public static String[] escapeExpressions(String args) {
  // special case for ' and " so we can allow expressions
  if (args.indexOf('\'') != -1)
    return escapeExpressions(args, "'");
  else if (args.indexOf('\"') != -1)
    return escapeExpressions(args, "\"");
  else
    return args.trim().split(" +");
}

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

Utils.warnUser(logger, String.format(
    "Rscript not found in environment path. %s will be generated but PDF plots will not.",
    RSCRIPT_FILE));
replicate.add(Utils.getRandomGenerator().nextDouble());

代码示例来源：origin: broadgsa/gatk

@BeforeMethod
public void initializeWalkerTests() {
  logger.debug("Initializing walker tests");
  Utils.resetRandomGenerator();
}

代码示例来源：origin: broadgsa/gatk

public static void warnUser(final String msg) {
  warnUser(logger, msg);
}

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

@Override
public String toString(int offset) {
  String off = offset > 0 ? Utils.dupString(' ', offset) : "";
  StringBuilder b = new StringBuilder();
  b.append("(").append("\n");
  Collection<DiffElement> atomicElts = getAtomicElements();
  for ( DiffElement elt : atomicElts ) {
    b.append(elt.toString(offset + 2)).append('\n');
  }
  for ( DiffElement elt : getCompoundElements() ) {
    b.append(elt.toString(offset + 4)).append('\n');
  }
  b.append(off).append(")").append("\n");
  return b.toString();
}

代码示例来源：origin: broadgsa/gatk

@DataProvider(name = "ArrayMinData")
public Object[][] makeArrayMinData() {
  List<Object[]> tests = new ArrayList<>();
  // this functionality can be adapted to provide input data for whatever you might want in your data
  tests.add(new Object[]{Arrays.asList(10), 10});
  tests.add(new Object[]{Arrays.asList(-10), -10});
  for ( final List<Integer> values : Utils.makePermutations(Arrays.asList(1,2,3), 3, false) ) {
    tests.add(new Object[]{values, 1});
  }
  for ( final List<Integer> values : Utils.makePermutations(Arrays.asList(1,2,-3), 3, false) ) {
    tests.add(new Object[]{values, -3});
  }
  return tests.toArray(new Object[][]{});
}

代码示例来源：origin: broadgsa/gatk

private List<String> getListArguments(File file) throws IOException {
  ArrayList<String> argsList = new ArrayList<String>();
  for (String line: FileUtils.readLines(file))
    argsList.addAll(Arrays.asList(Utils.escapeExpressions(line)));
  return argsList;
}

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "DownsamplingReadsIteratorTestDataProvider")
  public void runDownsamplingReadsIteratorTest( DownsamplingReadsIteratorTest test ) {
    logger.warn("Running test: " + test);

    Utils.resetRandomGenerator();
    test.run();
  }
}

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

/**
 * Checks whether the last-modification-time of the inputs is consistent with their relative roles.
 *
 * This routine does not thrown an exception but may output a warning message if inconsistencies are spotted.
 *
 * @param beforeFile the before report file.
 * @param afterFile  the after report file.
 */
private void checkInputReportFileLMT(final File beforeFile, final File afterFile) {
  if (ignoreLastModificationTime  || beforeFile == null || afterFile == null) {
    return; // nothing to do here
  } else if (beforeFile.lastModified() > afterFile.lastModified()) {
    Utils.warnUser("Last modification timestamp for 'Before' and 'After'"
        + "recalibration reports are in the wrong order. Perhaps, have they been swapped?");
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Provide an initial value for reduce computations.
 *
 * @return Initial value of reduce.
 */
public Integer reduceInit() {
  out.println(Utils.join(" \t", Arrays.asList("ReadGroup", "ReadLength", "NClippingEvents", "NClippedBases", "PercentClipped")));
  return 0;
}

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

/**
 * 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;
}