Program: 141158
Project: 141158
Buggy source:
private MapperProcess createMapperProcessPE(final String soapPath,final String archivePath,final File readsFile1,final File readsFile2,final File outputFile,final File unmapFile,final File unpairedFile,final GenomeDescription genomeDescription,final boolean fileMode) throws IOException {
  return new MapperProcess(this,true,false,true){
    @Override protected List<List<String>> createCommandLines(){
      final List<String> cmd=new ArrayList<String>();
      cmd.add(soapPath);
      if (getListMapperArguments() != null)       cmd.addAll(getListMapperArguments());
      cmd.add("String_Node_Str");
      cmd.add(getThreadsNumber() + "String_Node_Str");
      cmd.add("String_Node_Str");
      cmd.add(readsFile1.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(readsFile2.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(archivePath);
      cmd.add("String_Node_Str");
      cmd.add(outputFile.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(unmapFile.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(unpairedFile.getAbsolutePath());
      return Collections.singletonList(cmd);
    }
    @Override protected InputStream createCustomInputStream(    InputStream stdout) throws FileNotFoundException {
      return new SequenceInputStream(convertSOAP2SAM(stdout,genomeDescription,isPairedEnd()),convertFasta2SAM(new FileInputStream(unmapFile)));
    }
    @Override protected void clean(){
      outputFile.delete();
      unmapFile.delete();
    }
  }
;
}

Fixed version (ground truth):
private MapperProcess createMapperProcessPE(final String soapPath,final String archivePath,final File readsFile1,final File readsFile2,final File outputFile,final File unmapFile,final File unpairedFile,final GenomeDescription genomeDescription,final boolean fileMode) throws IOException {
  return new MapperProcess(this,true,false,true){
    @Override protected List<List<String>> createCommandLines(){
      final List<String> cmd=new ArrayList<String>();
      cmd.add(soapPath);
      if (getListMapperArguments() != null)       cmd.addAll(getListMapperArguments());
      cmd.add("String_Node_Str");
      cmd.add(getThreadsNumber() + "String_Node_Str");
      cmd.add("String_Node_Str");
      cmd.add(readsFile1.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(readsFile2.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(archivePath);
      cmd.add("String_Node_Str");
      cmd.add(outputFile.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(unmapFile.getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(unpairedFile.getAbsolutePath());
      return Collections.singletonList(cmd);
    }
    @Override protected InputStream createCustomInputStream(    InputStream stdout) throws FileNotFoundException {
      return new SequenceInputStream(convertSOAP2SAM(stdout,genomeDescription,isPairedEnd()),convertFasta2SAM(new FileInputStream(unmapFile)));
    }
    @Override protected void clean(){
      if (!outputFile.delete()) {
        getLogger().warning("String_Node_Str" + outputFile);
      }
      if (!unmapFile.delete()) {
        getLogger().warning("String_Node_Str" + unmapFile);
      }
    }
  }
;
}