Class VariantRealign


  • public class VariantRealign
    extends java.lang.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
    • Constructor Detail

      • VariantRealign

        public VariantRealign()
      • VariantRealign

        public VariantRealign​(Variant variant)
    • Method Detail

      • getAltRealign

        public java.lang.String getAltRealign()
      • getRefRealign

        public java.lang.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​(java.lang.String sequenceAlt)
      • setSequenceRef

        public void setSequenceRef​(java.lang.String sequenceRef)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object