Package picard.util

Class LiftoverUtils


  • public class LiftoverUtils
    extends Object
    • Constructor Summary

      Constructors 
      Constructor Description
      LiftoverUtils()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      protected static List<String> allelesToStringList​(List<htsjdk.variant.variantcontext.Allele> alleles)
      This is a utility method that will convert a list of alleles into a list of base strings.
      protected static htsjdk.variant.variantcontext.GenotypesContext fixGenotypes​(htsjdk.variant.variantcontext.GenotypesContext originals, List<htsjdk.variant.variantcontext.Allele> originalAlleles, List<htsjdk.variant.variantcontext.Allele> newAlleles)  
      protected static void leftAlignVariant​(htsjdk.variant.variantcontext.VariantContextBuilder builder, int start, int end, List<htsjdk.variant.variantcontext.Allele> alleles, htsjdk.samtools.reference.ReferenceSequence referenceSequence)
      Normalizes and left aligns a VariantContextBuilder.
      protected static htsjdk.variant.variantcontext.VariantContextBuilder liftSimpleVariantContext​(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target)  
      static htsjdk.variant.variantcontext.VariantContext liftVariant​(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq, boolean writeOriginalPosition, boolean writeOriginalAlleles)
      This will take an input VariantContext and lift to the provided interval.
      protected static htsjdk.variant.variantcontext.VariantContextBuilder reverseComplementVariantContext​(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq)  
      static htsjdk.variant.variantcontext.VariantContext swapRefAlt​(htsjdk.variant.variantcontext.VariantContext vc, Collection<String> annotationsToReverse, Collection<String> annotationsToDrop)
      method to swap the reference and alt alleles of a bi-allelic, SNP
    • Field Detail

      • SWAPPED_ALLELES

        public static final String SWAPPED_ALLELES
        Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
        See Also:
        Constant Field Values
      • DEFAULT_TAGS_TO_REVERSE

        public static final Collection<String> DEFAULT_TAGS_TO_REVERSE
        Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
      • DEFAULT_TAGS_TO_DROP

        public static final Collection<String> DEFAULT_TAGS_TO_DROP
      • log

        public static final htsjdk.samtools.util.Log log
    • Constructor Detail

      • LiftoverUtils

        public LiftoverUtils()
    • Method Detail

      • liftVariant

        public static htsjdk.variant.variantcontext.VariantContext liftVariant​(htsjdk.variant.variantcontext.VariantContext source,
                                                                               htsjdk.samtools.util.Interval target,
                                                                               htsjdk.samtools.reference.ReferenceSequence refSeq,
                                                                               boolean writeOriginalPosition,
                                                                               boolean writeOriginalAlleles)
        This will take an input VariantContext and lift to the provided interval. If this interval is in the opposite orientation, all alleles and genotypes will be reverse complemented and indels will be left-aligned. Currently this is only able to invert biallelic indels, and null will be returned for any unsupported VC.
        Parameters:
        source - The VariantContext to lift
        target - The target interval
        refSeq - The reference sequence, which should match the target interval
        writeOriginalPosition - If true, INFO field annotations will be added to store the original position and contig
        writeOriginalAlleles - If true, an INFO field annotation will be added to store the original alleles in order. This can be useful in the case of more complex liftovers, like reverse complements, left aligned indels or swapped REF/ALT
        Returns:
        The lifted VariantContext. This will be null if the input VariantContext could not be lifted.
      • allelesToStringList

        protected static List<String> allelesToStringList​(List<htsjdk.variant.variantcontext.Allele> alleles)
        This is a utility method that will convert a list of alleles into a list of base strings. Reference status is ignored when creating these strings (i.e. 'A', not 'A*'). These strings should be sufficient to recreate an Allele using Allele.create()
        Parameters:
        alleles - The list of alleles
        Returns:
        A list of strings representing the bases of the input alleles.
      • liftSimpleVariantContext

        protected static htsjdk.variant.variantcontext.VariantContextBuilder liftSimpleVariantContext​(htsjdk.variant.variantcontext.VariantContext source,
                                                                                                      htsjdk.samtools.util.Interval target)
      • reverseComplementVariantContext

        protected static htsjdk.variant.variantcontext.VariantContextBuilder reverseComplementVariantContext​(htsjdk.variant.variantcontext.VariantContext source,
                                                                                                             htsjdk.samtools.util.Interval target,
                                                                                                             htsjdk.samtools.reference.ReferenceSequence refSeq)
      • fixGenotypes

        protected static htsjdk.variant.variantcontext.GenotypesContext fixGenotypes​(htsjdk.variant.variantcontext.GenotypesContext originals,
                                                                                     List<htsjdk.variant.variantcontext.Allele> originalAlleles,
                                                                                     List<htsjdk.variant.variantcontext.Allele> newAlleles)
      • swapRefAlt

        public static htsjdk.variant.variantcontext.VariantContext swapRefAlt​(htsjdk.variant.variantcontext.VariantContext vc,
                                                                              Collection<String> annotationsToReverse,
                                                                              Collection<String> annotationsToDrop)
        method to swap the reference and alt alleles of a bi-allelic, SNP
        Parameters:
        vc - the VariantContext (bi-allelic SNP) that needs to have it's REF and ALT alleles swapped.
        annotationsToReverse - INFO field annotations (of double value) that will be reversed (x->1-x)
        annotationsToDrop - INFO field annotations that will be dropped from the result since they are invalid when REF and ALT are swapped
        Returns:
        a new VariantContext with alleles swapped, INFO fields modified and in the genotypes, GT, AD and PL corrected appropriately
      • leftAlignVariant

        protected static void leftAlignVariant​(htsjdk.variant.variantcontext.VariantContextBuilder builder,
                                               int start,
                                               int end,
                                               List<htsjdk.variant.variantcontext.Allele> alleles,
                                               htsjdk.samtools.reference.ReferenceSequence referenceSequence)
        Normalizes and left aligns a VariantContextBuilder. Note: this will modify the start/stop and alleles of this builder. Also note: if the reference allele does not match the reference sequence, this method will throw an exception Based on Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.