- liftOver
Lift over the given interval to the new genome build.
- <init>
Load UCSC chain file in order to lift over Intervals.
- createToInterval
- diagnosticLiftover
- targetIntersection
Add up overlap btw the blocks in this chain and the given interval.
- setLiftOverMinMatch
Set minimum fraction of bases that must remap.
- setShouldLogFailedIntervalsBelowThreshold
By default any lifted interval that falls below liftOverMinMatch will be logged.
Set this to false t
- validateToSequences
Throw an exception if all the "to" sequence names in the chains are not found in
the given sequence
- getContigMap
- resetFailedIntervalsBelowThresholdCounter
Resets the internal counter that tracks intervals that failed liftover due to
insufficient intersect