@Override
public void onTraversalDone(Long result) {
super.onTraversalDone(result);
out.println("Interval\tCallStatus\tCOV\tAVG");
for (GenomeLoc interval : intervalList) {
IntervalStatistics stats = intervalMap.get(interval);
out.println(
String.format(
"%s\t%s\t%d\t%f",
interval, stats.callableStatus(), stats.totalCoverage(), stats.averageCoverage()));
}
}
@Override
public void initialize() {
super.initialize();
if (intervalTrack == null)
throw new UserException("This tool currently only works if you provide an interval track");
parser =
new GenomeLocParser(
getToolkit()
.getMasterSequenceDictionary()); // Important to initialize the parser before
// creating the intervals below
List<GenomeLoc> originalList =
intervalTrack.getIntervals(
getToolkit()); // The original list of targets provided by the user that will be
// expanded or not depending on the options provided
intervalList = new TreeSet<GenomeLoc>(new GenomeLocComparator());
intervalMap = new HashMap<GenomeLoc, IntervalStatistics>(originalList.size() * 2);
for (GenomeLoc interval : originalList) addAndExpandIntervalToLists(interval);
intervalListIterator = intervalList.iterator();
}