String newErrMsg = "Ran out of lines in the syzyfile; further output of Syzygy power will be suppressed.";
outOfLinesInSyzyFile=true;
logger.warn(newErrMsg + " " + e.toString());
return new Pair(-1.1, "Printing Stops Here");
}
<BUG>String chromPos = null;
</BUG>
StringTokenizer lineTokenizer = new StringTokenizer(thisLine, pfFileDelimiter);
try {
<BUG>chromPos = lineTokenizer.nextToken();
</BUG>
for(int j = 1; j < colOffset; j++) {

String newErrMsg = "Ran out of lines in the syzyfile; further output of Syzygy power will be suppressed.";
outOfLinesInSyzyFile=true;
logger.warn(newErrMsg + " " + e.toString());
return new Pair(-1.1, "Printing Stops Here");
}
String chromPosTar = null;
StringTokenizer lineTokenizer = new StringTokenizer(thisLine, pfFileDelimiter);
try {
chromPosTar = lineTokenizer.nextToken();
for(int j = 1; j < colOffset; j++) {
