Program: 16790
Project: 16790
Buggy source:
/** 
 * Test of process method, of class GenbankReader.
 */
@Test public void testProcess() throws Throwable {
  GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader=new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("String_Node_Str"),"String_Node_Str",AminoAcidCompoundSet.getAminoAcidCompoundSet());
  ProteinSequence proteinSequence=new ProteinSequence(genbankProteinReader);
  genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(),proteinSequence);
  logger.info("String_Node_Str",proteinSequence.getAccession(),proteinSequence.getLength(),proteinSequence.getSequenceAsString().substring(0,10));
  GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader=new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("String_Node_Str"),"String_Node_Str",DNACompoundSet.getDNACompoundSet());
  DNASequence dnaSequence=new DNASequence(genbankDNAReader);
  genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(),dnaSequence);
  logger.info("String_Node_Str",dnaSequence.getAccession(),dnaSequence.getLength(),dnaSequence.getSequenceAsString().substring(0,10));
  File dnaFile=new File("String_Node_Str");
  File protFile=new File("String_Node_Str");
  LinkedHashMap<String,DNASequence> dnaSequences=GenbankReaderHelper.readGenbankDNASequence(dnaFile);
  for (  DNASequence sequence : dnaSequences.values()) {
    logger.info("String_Node_Str",sequence.getSequenceAsString());
  }
  LinkedHashMap<String,ProteinSequence> protSequences=GenbankReaderHelper.readGenbankProteinSequence(protFile);
  for (  ProteinSequence sequence : protSequences.values()) {
    logger.info("String_Node_Str",sequence.getSequenceAsString());
  }
  FileInputStream is=new FileInputStream(dnaFile);
  GenbankReader<DNASequence,NucleotideCompound> dnaReader=new GenbankReader<DNASequence,NucleotideCompound>(is,new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(),new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
  dnaSequences=dnaReader.process();
  is.close();
  logger.info("String_Node_Str",dnaSequences);
  is=new FileInputStream(protFile);
  GenbankReader<ProteinSequence,AminoAcidCompound> protReader=new GenbankReader<ProteinSequence,AminoAcidCompound>(is,new GenericGenbankHeaderParser<ProteinSequence,AminoAcidCompound>(),new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
  protSequences=protReader.process();
  is.close();
  logger.info("String_Node_Str",protSequences);
}

Fixed version (ground truth):
/** 
 * Test of process method, of class GenbankReader.
 */
@Test public void testProcess() throws Throwable {
  GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader=new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("String_Node_Str"),"String_Node_Str",AminoAcidCompoundSet.getAminoAcidCompoundSet());
  ProteinSequence proteinSequence=new ProteinSequence(genbankProteinReader);
  genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(),proteinSequence);
  logger.info("String_Node_Str",proteinSequence.getAccession(),proteinSequence.getLength(),proteinSequence.getSequenceAsString().substring(0,10));
  GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader=new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("String_Node_Str"),"String_Node_Str",DNACompoundSet.getDNACompoundSet());
  DNASequence dnaSequence=new DNASequence(genbankDNAReader);
  genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(),dnaSequence);
  logger.info("String_Node_Str",dnaSequence.getAccession(),dnaSequence.getLength(),dnaSequence.getSequenceAsString().substring(0,10));
  ClasspathResource dnaResource=new ClasspathResource("String_Node_Str",true);
  ClasspathResource protResource=new ClasspathResource("String_Node_Str");
  LinkedHashMap<String,DNASequence> dnaSequences=GenbankReaderHelper.readGenbankDNASequence(dnaResource.getInputStream());
  for (  DNASequence sequence : dnaSequences.values()) {
    logger.info("String_Node_Str",sequence.getSequenceAsString());
  }
  LinkedHashMap<String,ProteinSequence> protSequences=GenbankReaderHelper.readGenbankProteinSequence(protResource.getInputStream());
  for (  ProteinSequence sequence : protSequences.values()) {
    logger.info("String_Node_Str",sequence.getSequenceAsString());
  }
  GenbankReader<DNASequence,NucleotideCompound> dnaReader=new GenbankReader<DNASequence,NucleotideCompound>(dnaResource.getInputStream(),new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(),new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
  dnaSequences=dnaReader.process();
  logger.info("String_Node_Str",dnaSequences);
  GenbankReader<ProteinSequence,AminoAcidCompound> protReader=new GenbankReader<ProteinSequence,AminoAcidCompound>(protResource.getInputStream(),new GenericGenbankHeaderParser<ProteinSequence,AminoAcidCompound>(),new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
  protSequences=protReader.process();
  logger.info("String_Node_Str",protSequences);
}