Program: 12555
Project: 12555
Buggy source:
static void read(SBOLDocument SBOLDoc,InputStream in,String fileType) throws SBOLValidationException, IOException, SBOLConversionException {
  compliant=SBOLDoc.isCompliant();
  Scanner scanner=new Scanner(in,"String_Node_Str");
  String inputStreamString=scanner.useDelimiter("String_Node_Str").next();
  clearErrors();
  DocumentRoot<QName> document=null;
  try {
    if (FASTA.isFastaString(inputStreamString)) {
      SBOLDoc.setCreateDefaults(true);
      if (URIPrefix == null) {
        scanner.close();
        throw new SBOLConversionException("String_Node_Str");
      }
      SBOLDoc.setDefaultURIprefix(URIPrefix);
      FASTA.read(SBOLDoc,new BufferedReader(new StringReader(inputStreamString)),URIPrefix,version,defaultSequenceEncoding);
      scanner.close();
      return;
    }
 else     if (GenBank.isGenBankString(inputStreamString)) {
      SBOLDoc.setCreateDefaults(true);
      if (URIPrefix == null) {
        scanner.close();
        throw new SBOLConversionException("String_Node_Str");
      }
      SBOLDoc.setDefaultURIprefix(URIPrefix);
      GenBank.read(SBOLDoc,new BufferedReader(new StringReader(inputStreamString)),URIPrefix);
      scanner.close();
      return;
    }
 else     if (fileType.equals(SBOLDocument.JSON)) {
      document=readJSON(new StringReader(inputStreamString));
    }
 else     if (fileType.equals(SBOLDocument.TURTLE)) {
      document=readTurtle(new StringReader(inputStreamString));
    }
 else {
      document=readRDF(new StringReader(inputStreamString));
    }
    if (getSBOLVersion(document).equals(SBOLVERSION1)) {
      scanner.close();
      readV1(SBOLDoc,document);
      return;
    }
  }
 catch (  SBOLValidationException e) {
    if (keepGoing) {
      errors.add(e.getMessage());
      return;
    }
 else {
      throw new SBOLValidationException(e);
    }
  }
  for (  NamespaceBinding n : document.getNamespaceBindings()) {
    if (SBOLDoc.getNamespace(URI.create(n.getNamespaceURI())) == null) {
      if (n.getPrefix() == null) {
        SBOLDoc.addNamespaceBinding(NamespaceBinding(n.getNamespaceURI(),"String_Node_Str"));
      }
 else {
        SBOLDoc.addNamespaceBinding(NamespaceBinding(n.getNamespaceURI(),n.getPrefix()));
      }
    }
  }
  readTopLevelDocs(SBOLDoc,document);
  scanner.close();
  SBOLValidate.clearErrors();
  SBOLValidate.validateCompliance(SBOLDoc);
  if (SBOLValidate.getNumErrors() > 0) {
    SBOLDoc.setCompliant(false);
  }
}

Fixed version (ground truth):
static void read(SBOLDocument SBOLDoc,InputStream in,String fileType) throws SBOLValidationException, IOException, SBOLConversionException {
  compliant=SBOLDoc.isCompliant();
  Scanner scanner=new Scanner(in,"String_Node_Str");
  String inputStreamString=scanner.useDelimiter("String_Node_Str").next();
  clearErrors();
  DocumentRoot<QName> document=null;
  try {
    if (FASTA.isFastaString(inputStreamString)) {
      SBOLDoc.setCreateDefaults(true);
      SBOLDoc.setCompliant(true);
      if (URIPrefix == null) {
        scanner.close();
        throw new SBOLConversionException("String_Node_Str");
      }
      SBOLDoc.setDefaultURIprefix(URIPrefix);
      FASTA.read(SBOLDoc,inputStreamString,URIPrefix,version,defaultSequenceEncoding);
      scanner.close();
      return;
    }
 else     if (GenBank.isGenBankString(inputStreamString)) {
      SBOLDoc.setCreateDefaults(true);
      SBOLDoc.setCompliant(true);
      if (URIPrefix == null) {
        scanner.close();
        throw new SBOLConversionException("String_Node_Str");
      }
      SBOLDoc.setDefaultURIprefix(URIPrefix);
      GenBank.read(SBOLDoc,inputStreamString,URIPrefix);
      scanner.close();
      return;
    }
 else     if (fileType.equals(SBOLDocument.JSON)) {
      document=readJSON(new StringReader(inputStreamString));
    }
 else     if (fileType.equals(SBOLDocument.TURTLE)) {
      document=readTurtle(new StringReader(inputStreamString));
    }
 else {
      document=readRDF(new StringReader(inputStreamString));
    }
    if (getSBOLVersion(document).equals(SBOLVERSION1)) {
      scanner.close();
      readV1(SBOLDoc,document);
      return;
    }
  }
 catch (  SBOLValidationException e) {
    if (keepGoing) {
      errors.add(e.getMessage());
      return;
    }
 else {
      throw new SBOLValidationException(e);
    }
  }
  for (  NamespaceBinding n : document.getNamespaceBindings()) {
    if (SBOLDoc.getNamespace(URI.create(n.getNamespaceURI())) == null) {
      if (n.getPrefix() == null) {
        SBOLDoc.addNamespaceBinding(NamespaceBinding(n.getNamespaceURI(),"String_Node_Str"));
      }
 else {
        SBOLDoc.addNamespaceBinding(NamespaceBinding(n.getNamespaceURI(),n.getPrefix()));
      }
    }
  }
  readTopLevelDocs(SBOLDoc,document);
  scanner.close();
  SBOLValidate.clearErrors();
  SBOLValidate.validateCompliance(SBOLDoc);
  if (SBOLValidate.getNumErrors() > 0) {
    SBOLDoc.setCompliant(false);
  }
}