Program: 16830
Project: 16830
Buggy source:
public static void main(String[] args) throws Exception {
  String query="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
  String target="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
  GapPenalty penalty=new SimpleGapPenalty((short)-14,(short)-4);
  PairwiseSequenceAligner<DNASequence,NucleotideCompound> aligner=Alignments.getPairwiseAligner(new DNASequence(query,AmbiguityDNACompoundSet.getDNACompoundSet()),new DNASequence(target,AmbiguityDNACompoundSet.getDNACompoundSet()),PairwiseSequenceAlignerType.GLOBAL,penalty,SubstitutionMatrixHelper.getNuc4_4());
  SequencePair<DNASequence,NucleotideCompound> alignment=aligner.getPair();
  System.out.println("String_Node_Str" + alignment);
  int identical=alignment.getNumIdenticals();
  System.out.println("String_Node_Str" + identical);
  System.out.println("String_Node_Str" + identical / (float)query.length());
  System.out.println("String_Node_Str" + identical / (float)target.length());
}

Fixed version (ground truth):
public static void main(String[] args) throws Exception {
  String query="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
  String target="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
  GapPenalty penalty=new SimpleGapPenalty(-14,-4);
  PairwiseSequenceAligner<DNASequence,NucleotideCompound> aligner=Alignments.getPairwiseAligner(new DNASequence(query,AmbiguityDNACompoundSet.getDNACompoundSet()),new DNASequence(target,AmbiguityDNACompoundSet.getDNACompoundSet()),PairwiseSequenceAlignerType.GLOBAL,penalty,SubstitutionMatrixHelper.getNuc4_4());
  SequencePair<DNASequence,NucleotideCompound> alignment=aligner.getPair();
  System.out.println("String_Node_Str" + alignment);
  int identical=alignment.getNumIdenticals();
  System.out.println("String_Node_Str" + identical);
  System.out.println("String_Node_Str" + identical / (float)query.length());
  System.out.println("String_Node_Str" + identical / (float)target.length());
}