Package picard.util
Class LiftoverUtils
- java.lang.Object
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- picard.util.LiftoverUtils
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public class LiftoverUtils extends Object
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Field Summary
Fields Modifier and Type Field Description static Collection<String>
DEFAULT_TAGS_TO_DROP
static 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.static htsjdk.samtools.util.Log
log
static String
REV_COMPED_ALLELES
static 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.
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Constructor Summary
Constructors Constructor Description LiftoverUtils()
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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 aVariantContextBuilder
.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
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Field Detail
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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
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REV_COMPED_ALLELES
public static final String REV_COMPED_ALLELES
- See Also:
- Constant Field Values
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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.
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DEFAULT_TAGS_TO_DROP
public static final Collection<String> DEFAULT_TAGS_TO_DROP
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log
public static final htsjdk.samtools.util.Log log
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Method Detail
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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 lifttarget
- The target intervalrefSeq
- The reference sequence, which should match the target intervalwriteOriginalPosition
- If true, INFO field annotations will be added to store the original position and contigwriteOriginalAlleles
- 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.
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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.
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liftSimpleVariantContext
protected static htsjdk.variant.variantcontext.VariantContextBuilder liftSimpleVariantContext(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target)
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reverseComplementVariantContext
protected static htsjdk.variant.variantcontext.VariantContextBuilder reverseComplementVariantContext(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq)
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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)
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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
- theVariantContext
(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
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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 aVariantContextBuilder
. 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.
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