public final Map<String, IntervalTree<GenomeLoc>> createIntervalTreeByContig(
final IntervalBinding<Feature> intervals) {
final Map<String, IntervalTree<GenomeLoc>> byContig =
new HashMap<String, IntervalTree<GenomeLoc>>();
final List<GenomeLoc> locs = intervals.getIntervals(getToolkit());
// set up the map from contig -> interval tree
for (final String contig : getContigNames())
byContig.put(contig, new IntervalTree<GenomeLoc>());
for (final GenomeLoc loc : locs) {
byContig.get(loc.getContig()).put(loc.getStart(), loc.getStop(), loc);
}
return byContig;
}
@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();
}