Program: 189056
Project: 189056
Buggy source:
private void testFile(File testFile,boolean shouldSucceed){
  BufferedReader in=null;
  BufferedReader controlIn=null;
  try {
    File createTempFile=File.createTempFile("String_Node_Str","String_Node_Str");
    Assert.assertTrue("String_Node_Str",testFile.exists() && testFile.canRead());
    SGID main=SOFeatureImporter.runMain(new String[]{"String_Node_Str","String_Node_Str","String_Node_Str",adHocSet.getSGID().getRowKey(),"String_Node_Str",testFile.getAbsolutePath(),"String_Node_Str",createTempFile.getAbsolutePath(),"String_Node_Str",reference.getSGID().getRowKey(),"String_Node_Str",sequenceOntology.getSGID().getRowKey()});
    if (!shouldSucceed) {
      Assert.assertTrue(main == null);
      return;
    }
    VCFDumper.main(new String[]{main.getUuid().toString(),createTempFile.getAbsolutePath()});
    in=new BufferedReader(new FileReader(createTempFile));
    List<String> output=new ArrayList<String>();
    while (in.ready()) {
      String inLine=in.readLine();
      output.add(inLine);
    }
    Collections.sort(output);
    controlIn=new BufferedReader(new FileReader(testFile));
    List<String> control=new ArrayList<String>();
    while (controlIn.ready()) {
      control.add(controlIn.readLine());
    }
    Collections.sort(control);
    for (int i=0; i < output.size(); i++) {
      String[] cLine=control.get(i).split("String_Node_Str");
      String[] eLine=output.get(i).split("String_Node_Str");
      Assert.assertTrue("String_Node_Str",cLine[1].equals(eLine[1]));
      Assert.assertTrue("String_Node_Str",cLine[2].equals(eLine[2]));
      Assert.assertTrue("String_Node_Str",cLine[3].equals(eLine[3]));
      Assert.assertTrue("String_Node_Str",cLine[4].equals(eLine[4]));
      Assert.assertTrue("String_Node_Str",cLine[6].equals(eLine[6]));
      Assert.assertTrue("String_Node_Str",cLine[7].equals(eLine[7]));
    }
  }
 catch (  IOException ex) {
    Logger.getLogger(SOFeatureImporterTest.class.getName()).log(Level.SEVERE,null,ex);
    Assert.assertTrue("String_Node_Str",false);
  }
 finally {
    try {
      if (in != null) {
        in.close();
      }
      if (controlIn != null) {
        controlIn.close();
      }
    }
 catch (    IOException ex) {
      return;
    }
  }
}

Fixed version (ground truth):
private void testFile(File testFile,boolean shouldSucceed,boolean compressed){
  BufferedReader in=null;
  BufferedReader controlIn=null;
  try {
    File createTempFile=File.createTempFile("String_Node_Str","String_Node_Str");
    Assert.assertTrue("String_Node_Str",testFile.exists() && testFile.canRead());
    List<String> argList=new ArrayList<String>();
    argList.addAll(Arrays.asList(new String[]{"String_Node_Str","String_Node_Str","String_Node_Str",adHocSet.getSGID().getRowKey(),"String_Node_Str",testFile.getAbsolutePath(),"String_Node_Str",createTempFile.getAbsolutePath(),"String_Node_Str",reference.getSGID().getRowKey(),"String_Node_Str",sequenceOntology.getSGID().getRowKey()}));
    if (compressed) {
      argList.add("String_Node_Str");
    }
    SGID main=SOFeatureImporter.runMain(argList.toArray(new String[argList.size()]));
    if (!shouldSucceed) {
      Assert.assertTrue(main == null);
      return;
    }
    VCFDumper.main(new String[]{main.getUuid().toString(),createTempFile.getAbsolutePath()});
    in=new BufferedReader(new FileReader(createTempFile));
    List<String> output=new ArrayList<String>();
    while (in.ready()) {
      String inLine=in.readLine();
      output.add(inLine);
    }
    Collections.sort(output);
    if (compressed) {
      try {
        controlIn=VCFVariantImportWorker.handleCompressedInput(testFile.getAbsolutePath());
      }
 catch (      CompressorException ex) {
        Logger.getLogger(SOFeatureImporterTest.class.getName()).fatal(null,ex);
      }
catch (      FileNotFoundException ex) {
        Logger.getLogger(SOFeatureImporterTest.class.getName()).fatal(null,ex);
      }
    }
 else {
      controlIn=new BufferedReader(new FileReader(testFile));
    }
    List<String> control=new ArrayList<String>();
    String l;
    while ((l=controlIn.readLine()) != null) {
      control.add(l);
    }
    Collections.sort(control);
    for (int i=0; i < output.size(); i++) {
      String[] cLine=control.get(i).split("String_Node_Str");
      String[] eLine=output.get(i).split("String_Node_Str");
      Assert.assertTrue("String_Node_Str",cLine[1].equals(eLine[1]));
      Assert.assertTrue("String_Node_Str",cLine[2].equals(eLine[2]));
      Assert.assertTrue("String_Node_Str",cLine[3].equals(eLine[3]));
      Assert.assertTrue("String_Node_Str",cLine[4].equals(eLine[4]));
      Assert.assertTrue("String_Node_Str",cLine[6].equals(eLine[6]));
      Assert.assertTrue("String_Node_Str",cLine[7].equals(eLine[7]));
    }
  }
 catch (  IOException ex) {
    Logger.getLogger(SOFeatureImporterTest.class.getName()).fatal(null,ex);
    Assert.assertTrue("String_Node_Str",false);
  }
 finally {
    try {
      if (in != null) {
        in.close();
      }
      if (controlIn != null) {
        controlIn.close();
      }
    }
 catch (    IOException ex) {
      return;
    }
  }
}