public class LiftOver extends Object
Modifier and Type | Class | Description |
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static class |
LiftOver.PartialLiftover |
Represents a portion of a liftover operation, for use in diagnosing liftover failures.
|
Modifier and Type | Field | Description |
---|---|---|
static double |
DEFAULT_LIFTOVER_MINMATCH |
Constructor | Description |
---|---|
LiftOver(File chainFile) |
Load UCSC chain file in order to lift over Intervals.
|
Modifier and Type | Method | Description |
---|---|---|
List<LiftOver.PartialLiftover> |
diagnosticLiftover(Interval interval) |
|
Map<String,Set<String>> |
getContigMap() |
|
long |
getFailedIntervalsBelowThreshold() |
|
double |
getLiftOverMinMatch() |
Get minimum fraction of bases that must remap.
|
Interval |
liftOver(Interval interval) |
Lift over the given interval to the new genome build using the liftOverMinMatch set for this
LiftOver object.
|
Interval |
liftOver(Interval interval,
double liftOverMinMatch) |
Lift over the given interval to the new genome build.
|
void |
resetFailedIntervalsBelowThresholdCounter() |
Resets the internal counter that tracks intervals that failed liftover due to insufficient intersection length
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void |
setLiftOverMinMatch(double liftOverMinMatch) |
Set minimum fraction of bases that must remap.
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void |
setShouldLogFailedIntervalsBelowThreshold(boolean logFailedIntervals) |
By default any lifted interval that falls below liftOverMinMatch
will be logged.
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void |
validateToSequences(SAMSequenceDictionary sequenceDictionary) |
Throw an exception if all the "to" sequence names in the chains are not found in the given sequence dictionary.
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public static final double DEFAULT_LIFTOVER_MINMATCH
public LiftOver(File chainFile)
public void setShouldLogFailedIntervalsBelowThreshold(boolean logFailedIntervals)
logFailedIntervals
- public void resetFailedIntervalsBelowThresholdCounter()
public long getFailedIntervalsBelowThreshold()
public void validateToSequences(SAMSequenceDictionary sequenceDictionary)
public Interval liftOver(Interval interval)
interval
- Interval to be lifted over.public Interval liftOver(Interval interval, double liftOverMinMatch)
interval
- Interval to be lifted over.liftOverMinMatch
- Minimum fraction of bases that must remap.public List<LiftOver.PartialLiftover> diagnosticLiftover(Interval interval)
public Map<String,Set<String>> getContigMap()
public double getLiftOverMinMatch()
public void setLiftOverMinMatch(double liftOverMinMatch)