Program: 80623
Project: 80623
Buggy source:
public Variant parseLine(){
  String line=this.line;
  readLine();
  if (line == null || line.length() == 0) {
    return null;
  }
  if (isHeaderLine(line)) {
    return null;
  }
  String[] ll=line.split(DGV_COLUMN_SEPARATOR);
  final String var_id=ll[0];
  final ChrString chr=new ChrString(ll[1]);
  final int start_loc=Integer.parseInt(ll[2]);
  final int end_loc=Integer.parseInt(ll[3]);
  VariantType type=null;
  try {
    type=getVariantType(ll[4],ll[5]);
  }
 catch (  Exception e) {
    log.error(e.getMessage());
    return null;
  }
  int observedgains=(ll[15].length() > 0) ? Integer.parseInt(ll[15]) : 0;
  String REF;
  Alt[] alts=new Alt[1];
switch (type) {
case Deletion:
    byte[] temp=reference.byteRange(chr,start_loc,end_loc);
  if (temp != null) {
    REF=new String(temp);
  }
 else {
    log.error("String_Node_Str");
    log.error("String_Node_Str" + line);
    return null;
  }
alts[0]=new Alt(new FlexSeq());
break;
case Insertion:
REF="String_Node_Str";
alts[0]=new Alt(new FlexSeq(FlexSeq.Type.INS,end_loc - start_loc + 1));
break;
case Tandem_Duplication:
REF="String_Node_Str";
alts[0]=new Alt(new FlexSeq(FlexSeq.Type.TANDEM_DUP,end_loc - start_loc + 1,observedgains));
observedgains=Math.max(2,observedgains);
break;
case Inversion:
REF="String_Node_Str";
alts[0]=new Alt(new FlexSeq(FlexSeq.Type.INV,end_loc - start_loc + 1));
break;
default :
return null;
}
REF=REF.toUpperCase();
byte[] refs=new byte[REF.length()];
for (int i=0; i < REF.length(); i++) {
refs[i]=(byte)REF.charAt(i);
}
if (REF.length() == 1 && alts[0].length() == 1) {
return null;
}
 else if (REF.length() == 0 && alts[0].length() == 0) {
log.error("String_Node_Str");
log.error("String_Node_Str" + line);
return null;
}
byte[] phase={1,1};
return new Variant.Builder().chr(chr).pos(start_loc).referenceAlleleLength(refs.length).ref(refs).alts(alts).phase(phase).isPhased(false).varId(var_id).filter("String_Node_Str").refDeleted(String.valueOf((char)reference.byteAt(chr,start_loc - 1))).randomNumberGenerator(rand).build();
}

Fixed version (ground truth):
public Variant parseLine(){
  try {
    String line=this.line;
    readLine();
    if (line == null || line.length() == 0) {
      return null;
    }
    if (isHeaderLine(line)) {
      return null;
    }
    String[] ll=line.split(DGV_COLUMN_SEPARATOR);
    final String var_id=ll[0];
    final ChrString chr=new ChrString(ll[1]);
    final int start_loc=Integer.parseInt(ll[2]);
    final int end_loc=Integer.parseInt(ll[3]);
    VariantType type=getVariantType(ll[5].toLowerCase());
    int observedgains=(ll[15].length() > 0) ? Integer.parseInt(ll[15]) : 0;
    String REF;
    Alt[] alts=new Alt[1];
switch (type) {
case Deletion:
      byte[] temp=reference.byteRange(chr,start_loc,end_loc);
    if (temp != null) {
      REF=new String(temp);
    }
 else {
      log.error("String_Node_Str");
      log.error("String_Node_Str" + line);
      return null;
    }
  alts[0]=new Alt(new FlexSeq());
break;
case Insertion:
REF="String_Node_Str";
alts[0]=new Alt(new FlexSeq(FlexSeq.Type.INS,end_loc - start_loc + 1));
break;
case Tandem_Duplication:
REF="String_Node_Str";
alts[0]=new Alt(new FlexSeq(FlexSeq.Type.TANDEM_DUP,end_loc - start_loc + 1,observedgains));
observedgains=Math.max(2,observedgains);
break;
case Inversion:
REF="String_Node_Str";
alts[0]=new Alt(new FlexSeq(FlexSeq.Type.INV,end_loc - start_loc + 1));
break;
default :
return null;
}
REF=REF.toUpperCase();
byte[] refs=new byte[REF.length()];
for (int i=0; i < REF.length(); i++) {
refs[i]=(byte)REF.charAt(i);
}
if (REF.length() == 1 && alts[0].length() == 1) {
return null;
}
 else if (REF.length() == 0 && alts[0].length() == 0) {
log.error("String_Node_Str");
log.error("String_Node_Str" + line);
return null;
}
byte[] phase={1,1};
return new Variant.Builder().chr(chr).pos(start_loc).referenceAlleleLength(refs.length).ref(refs).alts(alts).phase(phase).isPhased(false).varId(var_id).filter("String_Node_Str").refDeleted(String.valueOf((char)reference.byteAt(chr,start_loc - 1))).randomNumberGenerator(rand).build();
}
 catch (Exception e) {
log.error(e.getMessage());
log.error("String_Node_Str" + line);
return null;
}
}