Program: 141423
Project: 141423
Buggy source:
private static void filterSamples(final File srcDesignFile,final File destDesignFile,final double threshold) throws IOException, EoulsanIOException {
  if (srcDesignFile == null)   throw new NullPointerException("String_Node_Str");
  if (destDesignFile == null)   throw new NullPointerException("String_Node_Str");
  if (destDesignFile.exists())   throw new EoulsanIOException("String_Node_Str" + destDesignFile);
  final DesignReader dr=new SimpleDesignReader(srcDesignFile);
  final Design design=dr.read();
  LogReader logReader=new LogReader(new File("String_Node_Str"));
  final Reporter filterReadsReporter=logReader.read();
  logReader=new LogReader(new File("String_Node_Str"));
  final Reporter soapMapReadsReporter=logReader.read();
  final Map<String,Long> sampleInputMapReads=parseReporter(filterReadsReporter,"String_Node_Str");
  final Map<String,Long> soapAlignementWithOneLocus=parseReporter(soapMapReadsReporter,"String_Node_Str");
  for (  String sample : sampleInputMapReads.keySet()) {
    if (!soapAlignementWithOneLocus.containsKey(sample))     continue;
    final long inputReads=sampleInputMapReads.get(sample);
    final long oneLocus=soapAlignementWithOneLocus.get(sample);
    final double ratio=(double)oneLocus / (double)inputReads;
    logger.info("String_Node_Str" + sample + "String_Node_Str"+ oneLocus+ "String_Node_Str"+ inputReads+ "String_Node_Str"+ ratio+ "String_Node_Str"+ threshold);
    if (ratio < threshold) {
      design.removeSample(sample);
      logger.info("String_Node_Str" + sample);
    }
  }
  DesignWriter writer=new SimpleDesignWriter(destDesignFile);
  writer.write(design);
}

Fixed version (ground truth):
private static void filterSamples(final File srcDesignFile,final File destDesignFile,final double threshold) throws IOException, EoulsanIOException {
  if (srcDesignFile == null)   throw new NullPointerException("String_Node_Str");
  if (destDesignFile == null)   throw new NullPointerException("String_Node_Str");
  if (destDesignFile.exists())   throw new EoulsanIOException("String_Node_Str" + destDesignFile);
  final DesignReader dr=new SimpleDesignReader(srcDesignFile);
  final Design design=dr.read();
  LogReader logReader=new LogReader(new File("String_Node_Str"));
  final Reporter filterReadsReporter=logReader.read();
  logReader=new LogReader(new File("String_Node_Str"));
  final Reporter soapMapReadsReporter=logReader.read();
  final Map<String,Long> sampleInputMapReads=parseReporter(filterReadsReporter,Common.READS_AFTER_FILTERING_COUNTER);
  final Map<String,Long> soapAlignementWithOneLocus=parseReporter(soapMapReadsReporter,Common.SOAP_ALIGNEMENT_WITH_ONLY_ONE_HIT_COUNTER);
  for (  String sample : sampleInputMapReads.keySet()) {
    if (!soapAlignementWithOneLocus.containsKey(sample))     continue;
    final long inputReads=sampleInputMapReads.get(sample);
    final long oneLocus=soapAlignementWithOneLocus.get(sample);
    final double ratio=(double)oneLocus / (double)inputReads;
    logger.info("String_Node_Str" + sample + "String_Node_Str"+ oneLocus+ "String_Node_Str"+ inputReads+ "String_Node_Str"+ ratio+ "String_Node_Str"+ threshold);
    if (ratio < threshold) {
      design.removeSample(sample);
      logger.info("String_Node_Str" + sample);
    }
  }
  DesignWriter writer=new SimpleDesignWriter(destDesignFile);
  writer.write(design);
}