Class VariantRealign

java.lang.Object
org.snpeff.align.VariantRealign

public class VariantRealign extends Object
Re-align a variant towards the leftmost (rightmost) position Note: We perform a 'progressive' realignment, asking for more reference sequence as we need it
Author:
pcingola
  • Field Details

  • Constructor Details

    • VariantRealign

      public VariantRealign()
    • VariantRealign

      public VariantRealign(Variant variant)
  • Method Details

    • getAltRealign

      public String getAltRealign()
    • getRefRealign

      public String getRefRealign()
    • getVariantRealigned

      public Variant getVariantRealigned()
    • realign

      public boolean realign()
      Realign variant
      Returns:
      true if variant was realigned and a new variant (different than the original one) was created. false if it wasn't realigned or there was an error
    • realignSeqs

      public void realignSeqs()
      Realignment
    • setAlignLeft

      public void setAlignLeft()
    • setAlignRight

      public void setAlignRight()
    • setDebug

      public void setDebug(boolean debug)
    • setSequenceAlt

      public void setSequenceAlt(String sequenceAlt)
    • setSequenceRef

      public void setSequenceRef(String sequenceRef)
    • toString

      public String toString()
      Overrides:
      toString in class Object