Package htsjdk.samtools.liftover

Class LiftOver

java.lang.Object
htsjdk.samtools.liftover.LiftOver
public class LiftOver extends 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.

  • Field Details

    • DEFAULT_LIFTOVER_MINMATCH

      public static final double DEFAULT_LIFTOVER_MINMATCH
      See Also:

  • Constructor Details

    • LiftOver

      public LiftOver(File chainFile)
      Load UCSC chain file in order to lift over Intervals.

    • LiftOver

      public LiftOver(InputStream chainFileInputStream, String sourceName)
      Load UCSC chain file in order to lift over Intervals.

  • Method Details

    • setShouldLogFailedIntervalsBelowThreshold

      public void setShouldLogFailedIntervalsBelowThreshold(boolean logFailedIntervals)
      By default any lifted interval that falls below liftOverMinMatch will be logged. Set this to false to prevent logging.
      Parameters:
      logFailedIntervals -

    • resetFailedIntervalsBelowThresholdCounter

      public void resetFailedIntervalsBelowThresholdCounter()
      Resets the internal counter that tracks intervals that failed liftover due to insufficient intersection length

    • getFailedIntervalsBelowThreshold

      public long getFailedIntervalsBelowThreshold()
      Returns:
      The total number of intervals that have failed liftover due to insufficient intersection length

    • 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 List<LiftOver.PartialLiftover> diagnosticLiftover(Interval interval)

    • getContigMap

      public Map<String,Set<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.