public SpliceJunctionHelper.LoadOptions getSpliceJunctionLoadOptions() {
return loadOptions;
}
public void setMinJunctionCoverage(int minJunctionCoverage) {
this.loadOptions = new SpliceJunctionHelper.LoadOptions(minJunctionCoverage, this.loadOptions.minReadFlankingWidth);
<BUG>for (AlignmentInterval interval : getLoadedIntervals()) {
</BUG>
interval.getSpliceJunctionHelper().setLoadOptions(this.loadOptions);
}
}

public SpliceJunctionHelper.LoadOptions getSpliceJunctionLoadOptions() {
return loadOptions;
}
public void setMinJunctionCoverage(int minJunctionCoverage) {
this.loadOptions = new SpliceJunctionHelper.LoadOptions(minJunctionCoverage, this.loadOptions.minReadFlankingWidth);
for (AlignmentInterval interval : intervalCache.values()) {
interval.getSpliceJunctionHelper().setLoadOptions(this.loadOptions);
}
}
