- <init>
Constructs a new interval list using the supplied header information.
- add
Adds an interval to the list of intervals.
- fromFile
Parses an interval list from a file.
- getIntervals
Gets the set of intervals as held internally.
- concatenate
A utility function for merging a list of IntervalLists, checks for equal
dictionaries. Merging does
- getHeader
Gets the header (if there is one) for the interval list.
- invert
inverts an IntervalList and returns one that has exactly all the bases in the
dictionary that the or
- uniqued
Returned an independent IntervalList that is sorted and uniquified.
- addall
Adds a Collection of intervals to the list of intervals.
- getBaseCount
Gets the (potentially redundant) sum of the length of the intervals in the list.
- intersection
A utility function for intersecting a list of IntervalLists, checks for equal
dictionaries.
- overlaps
A utility function for finding the intervals in the first list that have at
least 1bp overlap with a