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

Utils.escapeExpressions介绍

[英]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.
[中]将命令参数中的表达式按空格拆分，并返回表达式数组。表达式可以使用单引号或双引号对任何单个表达式进行分组，但不能同时使用两个引号。

代码示例

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

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

actual = Utils.escapeExpressions("one two three");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions(" one two three");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("one two three ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions(" one two three ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("  one  two  three  ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("one two 'three four' five six");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions(" one two 'three four' five six");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("one two 'three four' five six ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions(" one two 'three four' five six ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("  one  two  'three four'  five  six  ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("'one two' three four");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions(" 'one two' three four");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions("'one two' three four ");
Assert.assertEquals(actual, expected);
actual = Utils.escapeExpressions(" 'one two' three four ");

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "MismatchedExtensionsTest", expectedExceptions = IOException.class)
public void testMismatchedExtensions1(final String extension1, final String extension2) throws IOException {
  String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s -out %s",
      StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
      CatVariants.class.getCanonicalName(),
      BaseTest.b37KGReference,
      new File(CatVariantsDir, "CatVariantsTest1" + extension1),
      new File(CatVariantsDir, "CatVariantsTest2" + extension2),
      BaseTest.createTempFile("CatVariantsTest", ".bcf"));
  ProcessController pc = ProcessController.getThreadLocal();
  ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
  pc.execAndCheck(ps);
}

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "MismatchedExtensionsTest", expectedExceptions = IOException.class)
public void testMismatchedExtensions2(final String extension1, final String extension2) throws IOException {
  String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s -out %s",
      StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
      CatVariants.class.getCanonicalName(),
      BaseTest.b37KGReference,
      new File(CatVariantsDir, "CatVariantsTest1" + extension1),
      new File(CatVariantsDir, "CatVariantsTest2" + extension2),
      BaseTest.createTempFile("CatVariantsTest", ".vcf"));
  ProcessController pc = ProcessController.getThreadLocal();
  ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
  pc.execAndCheck(ps);
}

代码示例来源：origin: broadgsa/gatk

@Test()
  public void testCatVariantsGVCFGzIndexCreation() throws IOException{

    String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s -out %s",
        StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
        CatVariants.class.getCanonicalName(),
        BaseTest.b37KGReference,
        CatVariantsVcf1,
        CatVariantsVcf2,
        BaseTest.createTempFile("CatVariantsGVCFIndexCreationTest", "." + GATKVCFUtils.GVCF_GZ_EXT));

    ProcessController pc = ProcessController.getThreadLocal();
    ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
    pc.execAndCheck(ps);
  }
}

代码示例来源：origin: broadgsa/gatk

@Test()
public void testCatVariantsGVCFIndexCreation() throws IOException{
  String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s -out %s",
      StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
      CatVariants.class.getCanonicalName(),
      BaseTest.b37KGReference,
      CatVariantsVcf1,
      CatVariantsVcf2,
      BaseTest.createTempFile("CatVariantsGVCFIndexCreationTest", "." + GATKVCFUtils.GVCF_EXT));
  ProcessController pc = ProcessController.getThreadLocal();
  ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
  pc.execAndCheck(ps);
}

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "IndexDataProvider")
public void testCatVariantsVCFIndexCreation(VCFIndexCreatorTest testSpec) throws IOException{
  String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s --variant_index_type %s --variant_index_parameter %s -out %s",
      StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
      CatVariants.class.getCanonicalName(),
      BaseTest.b37KGReference,
      CatVariantsVcf1,
      CatVariantsVcf2,
      testSpec.type,
      testSpec.parameter,
      BaseTest.createTempFile("CatVariantsVCFIndexCreationTest", ".vcf"));
  ProcessController pc = ProcessController.getThreadLocal();
  ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
  pc.execAndCheck(ps);
}

代码示例来源：origin: broadgsa/gatk

String[] command = Utils.escapeExpressions(args);

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "SortOrderTest")
public void testSortOrder(final CatVariantsTestProvider cfg) throws IOException {
  ProcessController pc = ProcessController.getThreadLocal();
  ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cfg.getCmdLine()));
  pc.execAndCheck(ps);
  MD5DB.MD5Match result = md5db.testFileMD5("testSortOrder", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
  if(result.failed) {
    final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
    Assert.fail(failure.toString());
  }
}

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "ExtensionsTest")
public void testExtensions(final CatVariantsTestProvider cfg) throws IOException {
  ProcessController pc = ProcessController.getThreadLocal();
  ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cfg.getCmdLine()));
  pc.execAndCheck(ps);
  MD5DB.MD5Match result = md5db.testFileMD5("testExtensions", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
  if(result.failed) {
    final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
    Assert.fail(failure.toString());
  }
}