Package org.broadinstitute.hellbender.utils.smithwaterman

Class SWNativeAlignerWrapper

java.lang.Object
org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper
All Implemented Interfaces:
Closeable, AutoCloseable, SmithWatermanAligner
public final class SWNativeAlignerWrapper extends Object implements SmithWatermanAligner
A wrapper that converts instances of SWAlignerNativeBinding into a SmithWatermanAligner

  • Nested Class Summary

    Nested classes/interfaces inherited from interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner

    SmithWatermanAligner.Implementation

  • Field Summary

    Fields inherited from interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner

    logger

  • Constructor Summary

    Constructors
    Constructor
    Description
    SWNativeAlignerWrapper(org.broadinstitute.gatk.nativebindings.smithwaterman.SWAlignerNativeBinding aligner)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    SmithWatermanAlignment
    align(byte[] reference, byte[] alternate, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters parameters, org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy overhangStrategy)
    perform a Smith-Waterman alignment of alt against ref
    void
    close()
    Report total compute time and close aligner

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • SWNativeAlignerWrapper

      public SWNativeAlignerWrapper(org.broadinstitute.gatk.nativebindings.smithwaterman.SWAlignerNativeBinding aligner)

  • Method Details

    • align

      public SmithWatermanAlignment align(byte[] reference, byte[] alternate, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters parameters, org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy overhangStrategy)
      Description copied from interface: SmithWatermanAligner
      perform a Smith-Waterman alignment of alt against ref
      Specified by:
      align in interface SmithWatermanAligner
      Parameters:
      reference - bases to align to, values must be the byte equivalent of uppercase chars
      alternate - bases to align against ref, values must be the byte equivalent of uppercase chars
      parameters - a set of weights to use when performing the alignment
      overhangStrategy - how to treat overhangs during alignment

    • close

      public void close()
      Report total compute time and close aligner
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface SmithWatermanAligner