htsjdk.samtools.liftover

Class LiftOver

java.lang.Object

htsjdk.samtools.liftover.LiftOver

public class LiftOver
extends java.lang.Object

Java port of UCSC liftOver. Only the most basic liftOver functionality is implemented. Internally coordinates are 0-based, half-open. The API is standard Picard 1-based, inclusive.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	LiftOver.PartialLiftover Represents a portion of a liftover operation, for use in diagnosing liftover failures.

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_LIFTOVER_MINMATCH

Constructor Summary

Constructors

Constructor and Description
LiftOver(java.io.File chainFile) Load UCSC chain file in order to lift over Intervals.

Method Summary

Modifier and Type	Method and Description
java.util.List<LiftOver.PartialLiftover>	diagnosticLiftover(Interval interval)
java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	getContigMap()
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	setLiftOverMinMatch(double liftOverMinMatch) Set minimum fraction of bases that must remap.
void	validateToSequences(SAMSequenceDictionary sequenceDictionary) Throw an exception if all the "to" sequence names in the chains are not found in the given sequence dictionary.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_LIFTOVER_MINMATCH

public static final double DEFAULT_LIFTOVER_MINMATCH

See Also:

Constant Field Values

Constructor Detail

LiftOver

public LiftOver(java.io.File chainFile)

Load UCSC chain file in order to lift over Intervals.

Method Detail

validateToSequences

public void validateToSequences(SAMSequenceDictionary sequenceDictionary)

Throw an exception if all the "to" sequence names in the chains are not found in the given sequence dictionary.

liftOver

public Interval liftOver(Interval interval)

Lift over the given interval to the new genome build using the liftOverMinMatch set for this LiftOver object.

Parameters:

interval - Interval to be lifted over.

Returns:

Interval in the output build coordinates, or null if it cannot be lifted over.

liftOver

public Interval liftOver(Interval interval,
                         double liftOverMinMatch)

Lift over the given interval to the new genome build.

Parameters:

interval - Interval to be lifted over.

liftOverMinMatch - Minimum fraction of bases that must remap.

Returns:

Interval in the output build coordinates, or null if it cannot be lifted over.

diagnosticLiftover

public java.util.List<LiftOver.PartialLiftover> diagnosticLiftover(Interval interval)

getContigMap

public java.util.Map<java.lang.String,java.util.Set<java.lang.String>> getContigMap()

Returns:

the set of destination contigs for each source contig in the chains file.

getLiftOverMinMatch

public double getLiftOverMinMatch()

Get minimum fraction of bases that must remap.

setLiftOverMinMatch

public void setLiftOverMinMatch(double liftOverMinMatch)

Set minimum fraction of bases that must remap.