Genotype

java.lang.Object
- htsjdk.variant.variantcontext.Genotype

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<Genotype>

Direct Known Subclasses:

FastGenotype
```
public abstract class Genotype
extends java.lang.Object
implements java.lang.Comparable<Genotype>, java.io.Serializable
```
This class encompasses all the basic information about a genotype. It is immutable.

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`PHASED_ALLELE_SEPARATOR`
`static java.util.Collection<java.lang.String>`	`PRIMARY_KEYS` A list of genotype field keys corresponding to values we manage inline in the Genotype object.
`static long`	`serialVersionUID`
`static java.lang.String`	`UNPHASED_ALLELE_SEPARATOR`

Constructor Summary

Constructors
Modifier Constructor and Description

protected Genotype(java.lang.String sampleName, java.lang.String filters)

Constructors
Modifier	Constructor and Description
`protected`	`Genotype(java.lang.String sampleName, java.lang.String filters)`

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`compareTo(Genotype genotype)` comparable genotypes -> compareTo on the sample names
`int`	`countAllele(Allele allele)` Returns how many times allele appears in this genotype object?
`protected GenotypeType`	`determineType()` Internal code to determine the type of the genotype from the alleles vector
`abstract int[]`	`getAD()`
`abstract Allele`	`getAllele(int i)` Get the ith allele in this genotype
`abstract java.util.List<Allele>`	`getAlleles()`
`protected java.util.List<java.lang.String>`	`getAlleleStrings()` Utility that returns a list of allele strings corresponding to the alleles in this sample
`java.lang.Object`	`getAnyAttribute(java.lang.String key)` A totally generic getter, that allows you to specific keys that correspond to even inline values (GQ, for example).
`double`	`getAttributeAsDouble(java.lang.String key, double defaultValue)` Deprecated.
`int`	`getAttributeAsInt(java.lang.String key, int defaultValue)` Deprecated.
`java.lang.String`	`getAttributeAsString(java.lang.String key, java.lang.String defaultValue)` Deprecated.
`abstract int`	`getDP()`
`java.lang.Object`	`getExtendedAttribute(java.lang.String key)` Same as #getExtendedAttribute with a null default
`java.lang.Object`	`getExtendedAttribute(java.lang.String key, java.lang.Object defaultValue)` Get the extended attribute value associated with key, if possible
`abstract java.util.Map<java.lang.String,java.lang.Object>`	`getExtendedAttributes()` Returns the extended attributes for this object
`java.lang.String`	`getFilters()` Returns the filter string associated with this Genotype.
`java.lang.String`	`getGenotypeString()` Return a VCF-like string representation for the alleles of this genotype.
`java.lang.String`	`getGenotypeString(boolean ignoreRefState)` Return a VCF-like string representation for the alleles of this genotype.
`abstract int`	`getGQ()` Returns a phred-scaled quality score, or -1 if none is available
`GenotypeLikelihoods`	`getLikelihoods()` Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing
`java.lang.String`	`getLikelihoodsString()` Convenience function that returns a string representation of the PL field of this genotype, or .
`double`	`getLog10PError()` Deprecated.
`int`	`getPhredScaledQual()` Deprecated.
`abstract int[]`	`getPL()` Unsafe low-level accessor the PL field itself, may be null.
`int`	`getPloidy()` What is the ploidy of this sample?
`java.lang.String`	`getSampleName()` Returns the name associated with this sample.
`GenotypeType`	`getType()`
`boolean`	`hasAD()` Does the AD field have a value?
`boolean`	`hasAnyAttribute(java.lang.String key)`
`boolean`	`hasDP()` Does the DP field have a value?
`boolean`	`hasExtendedAttribute(java.lang.String key)` Is key associated with a value (even a null one) in the extended attributes? Note this will not return true for the inline attributes DP, GQ, AD, or PL
`protected static boolean`	`hasForbiddenKey(java.util.Map<java.lang.String,java.lang.Object> attributes)` Does the attribute map have a mapping involving a forbidden key (i.e., one that's managed inline by this Genotypes object?
`boolean`	`hasGQ()` Does the GQ field have a value?
`boolean`	`hasLikelihoods()`
`boolean`	`hasLog10PError()` Deprecated.
`boolean`	`hasPL()` Does the PL field have a value?
`boolean`	`isAvailable()`
`boolean`	`isCalled()`
`boolean`	`isFiltered()` Is this genotype filtered or not?
`protected static boolean`	`isForbiddenKey(java.lang.String key)`
`boolean`	`isHet()`
`boolean`	`isHetNonRef()`
`boolean`	`isHom()`
`boolean`	`isHomRef()`
`boolean`	`isHomVar()`
`boolean`	`isMixed()`
`boolean`	`isNoCall()`
`boolean`	`isNonInformative()` Are all likelihoods for this sample non-informative? Returns true if all PLs are 0 => 0,0,0 => true 0,0,0,0,0,0 => true 0,10,100 => false
`abstract boolean`	`isPhased()` Are the alleles phased w.r.t.
`boolean`	`sameGenotype(Genotype other)`
`boolean`	`sameGenotype(Genotype other, boolean ignorePhase)`
`protected static <T extends java.lang.Comparable<T>,V> java.lang.String`	`sortedString(java.util.Map<T,V> c)` a utility method for generating sorted strings from a map key set.
`java.lang.String`	`toBriefString()`
`java.lang.String`	`toString()`
`protected static java.lang.String`	`toStringIfExists(java.lang.String name, int v)` Returns a display name for field name with value v if this isn't -1.
`protected static java.lang.String`	`toStringIfExists(java.lang.String name, int[] vs)` Returns a display name for field name with values vs if this isn't null.
`protected static java.lang.String`	`toStringIfExists(java.lang.String name, java.lang.String v)` Returns a display name for field name with String value v if this isn't null.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - serialVersionUID
```
public static final long serialVersionUID
```
    See Also:
    Constant Field Values
  - PRIMARY_KEYS
```
public static final java.util.Collection<java.lang.String> PRIMARY_KEYS
```
    A list of genotype field keys corresponding to values we manage inline in the Genotype object. They must not appear in the extended attributes map
  - PHASED_ALLELE_SEPARATOR
```
public static final java.lang.String PHASED_ALLELE_SEPARATOR
```
    See Also:
    Constant Field Values
  - UNPHASED_ALLELE_SEPARATOR
```
public static final java.lang.String UNPHASED_ALLELE_SEPARATOR
```
    See Also:
    Constant Field Values
- Constructor Detail
  - Genotype
```
protected Genotype(java.lang.String sampleName,
        java.lang.String filters)
```
- Method Detail
  - getAlleles
```
public abstract java.util.List<Allele> getAlleles()
```
    Returns:
    the alleles for this genotype. Cannot be null. May be empty
  - countAllele
```
public int countAllele(Allele allele)
```
    Returns how many times allele appears in this genotype object?
    
    Parameters:
    allele -
    
    Returns:
    a value >= 0 indicating how many times the allele occurred in this sample's genotype
  - getAllele
```
public abstract Allele getAllele(int i)
```
    Get the ith allele in this genotype
    
    Parameters:
    i - the ith allele, must be < the ploidy, starting with 0
    
    Returns:
    the allele at position i, which cannot be null
  - isPhased
```
public abstract boolean isPhased()
```
    Are the alleles phased w.r.t. the global phasing system?
    
    Returns:
    true if yes
  - getPloidy
```
public int getPloidy()
```
    What is the ploidy of this sample?
    
    Returns:
    the ploidy of this genotype. 0 if the site is no-called.
  - getDP
```
public abstract int getDP()
```
    Returns:
    the sequencing depth of this sample, or -1 if this value is missing
  - getAD
```
public abstract int[] getAD()
```
    Returns:
    the count of reads, one for each allele in the surrounding Variant context, matching the corresponding allele, or null if this value is missing. MUST NOT BE MODIFIED!
  - getSampleName
```
public java.lang.String getSampleName()
```
    Returns the name associated with this sample.
    
    Returns:
    a non-null String
  - getGQ
```
public abstract int getGQ()
```
    Returns a phred-scaled quality score, or -1 if none is available
    
    Returns:
  - hasPL
```
public boolean hasPL()
```
    Does the PL field have a value?
    
    Returns:
    true if there's a PL field value
  - hasAD
```
public boolean hasAD()
```
    Does the AD field have a value?
    
    Returns:
    true if there's a AD field value
  - hasGQ
```
public boolean hasGQ()
```
    Does the GQ field have a value?
    
    Returns:
    true if there's a GQ field value
  - hasDP
```
public boolean hasDP()
```
    Does the DP field have a value?
    
    Returns:
    true if there's a DP field value
  - getType
```
public GenotypeType getType()
```
    Returns:
    the high-level type of this sample's genotype
  - determineType
```
protected GenotypeType determineType()
```
    Internal code to determine the type of the genotype from the alleles vector
    
    Returns:
    the type
  - isHom
```
public boolean isHom()
```
    Returns:
    true if all observed alleles are the same (regardless of whether they are ref or alt); if any alleles are no-calls, this method will return false.
  - isHomRef
```
public boolean isHomRef()
```
    Returns:
    true if all observed alleles are ref; if any alleles are no-calls, this method will return false.
  - isHomVar
```
public boolean isHomVar()
```
    Returns:
    true if all observed alleles are alt; if any alleles are no-calls, this method will return false.
  - isHet
```
public boolean isHet()
```
    Returns:
    true if we're het (observed alleles differ); if the ploidy is less than 2 or if any alleles are no-calls, this method will return false.
  - isHetNonRef
```
public boolean isHetNonRef()
```
    Returns:
    true if we're het (observed alleles differ) and neither allele is reference; if the ploidy is less than 2 or if any alleles are no-calls, this method will return false.
  - isNoCall
```
public boolean isNoCall()
```
    Returns:
    true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF); if any alleles are not no-calls (even if some are), this method will return false.
  - isCalled
```
public boolean isCalled()
```
    Returns:
    true if this genotype is comprised of any alleles that are not no-calls (even if some are).
  - isMixed
```
public boolean isMixed()
```
    Returns:
    true if this genotype is comprised of both calls and no-calls.
  - isAvailable
```
public boolean isAvailable()
```
    Returns:
    true if the type of this genotype is set.
  - hasLikelihoods
```
public boolean hasLikelihoods()
```
    Returns:
    Returns true if this Genotype has PL field values
  - getLikelihoodsString
```
public java.lang.String getLikelihoodsString()
```
    Convenience function that returns a string representation of the PL field of this genotype, or . if none is available.
    
    Returns:
    a non-null String representation for the PL of this sample
  - getLikelihoods
```
public GenotypeLikelihoods getLikelihoods()
```
    Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing
    
    Returns:
    null or a GenotypesLikelihood object for this sample's PL field
  - isNonInformative
```
public boolean isNonInformative()
```
    Are all likelihoods for this sample non-informative? Returns true if all PLs are 0 => 0,0,0 => true 0,0,0,0,0,0 => true 0,10,100 => false
    
    Returns:
    true if all samples PLs are equal and == 0
  - getPL
```
public abstract int[] getPL()
```
    Unsafe low-level accessor the PL field itself, may be null.
    
    Returns:
    a pointer to the underlying PL data. MUST NOT BE MODIFIED!
  - getGenotypeString
```
public java.lang.String getGenotypeString()
```
    Return a VCF-like string representation for the alleles of this genotype. Does not append the reference * marker on the alleles.
    
    Returns:
    a string representing the genotypes, or null if the type is unavailable.
  - getGenotypeString
```
public java.lang.String getGenotypeString(boolean ignoreRefState)
```
    Return a VCF-like string representation for the alleles of this genotype. If ignoreRefState is true, will not append the reference * marker on the alleles.
    
    Returns:
    a string representing the genotypes, or null if the type is unavailable.
  - getAlleleStrings
```
protected java.util.List<java.lang.String> getAlleleStrings()
```
    Utility that returns a list of allele strings corresponding to the alleles in this sample
    
    Returns:
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - toBriefString
```
public java.lang.String toBriefString()
```
  - compareTo
```
public int compareTo(Genotype genotype)
```
    comparable genotypes -> compareTo on the sample names
    
    Specified by:
    
    compareTo in interface java.lang.Comparable<Genotype>
    
    Parameters:
    genotype -
    
    Returns:
  - sameGenotype
```
public boolean sameGenotype(Genotype other)
```
  - sameGenotype
```
public boolean sameGenotype(Genotype other,
                   boolean ignorePhase)
```
  - getExtendedAttributes
```
public abstract java.util.Map<java.lang.String,java.lang.Object> getExtendedAttributes()
```
    Returns the extended attributes for this object
    
    Returns:
    is never null, but is often isEmpty()
  - hasExtendedAttribute
```
public boolean hasExtendedAttribute(java.lang.String key)
```
    Is key associated with a value (even a null one) in the extended attributes? Note this will not return true for the inline attributes DP, GQ, AD, or PL
    
    Parameters:
    key - a non-null string key to check for an association
    
    Returns:
    true if key has a value in the extendedAttributes
  - getExtendedAttribute
```
public java.lang.Object getExtendedAttribute(java.lang.String key,
                                    java.lang.Object defaultValue)
```
    Get the extended attribute value associated with key, if possible
    
    Parameters:
    key - a non-null string key to fetch a value for
    defaultValue - the value to return if key isn't in the extended attributes
    
    Returns:
    a value (potentially) null associated with key, or defaultValue if no association exists
  - getExtendedAttribute
```
public java.lang.Object getExtendedAttribute(java.lang.String key)
```
    Same as #getExtendedAttribute with a null default
    
    Parameters:
    key -
    
    Returns:
  - getFilters
```
public final java.lang.String getFilters()
```
    Returns the filter string associated with this Genotype.
    
    Returns:
    If this result == null, then the genotype is considered PASSing filters If the result != null, then the genotype has failed filtering for the reason(s) specified in result. To be reference compliant multiple filter field string values can be encoded with a ; separator.
  - isFiltered
```
public final boolean isFiltered()
```
    Is this genotype filtered or not?
    
    Returns:
    returns false if getFilters() == null
  - hasLog10PError
```
@Deprecated
public boolean hasLog10PError()
```
    Deprecated.
  - getLog10PError
```
@Deprecated
public double getLog10PError()
```
    Deprecated.
  - getPhredScaledQual
```
@Deprecated
public int getPhredScaledQual()
```
    Deprecated.
  - getAttributeAsString
```
@Deprecated
public java.lang.String getAttributeAsString(java.lang.String key,
                                               java.lang.String defaultValue)
```
    Deprecated.
  - getAttributeAsInt
```
@Deprecated
public int getAttributeAsInt(java.lang.String key,
                               int defaultValue)
```
    Deprecated.
  - getAttributeAsDouble
```
@Deprecated
public double getAttributeAsDouble(java.lang.String key,
                                     double defaultValue)
```
    Deprecated.
  - getAnyAttribute
```
public java.lang.Object getAnyAttribute(java.lang.String key)
```
    A totally generic getter, that allows you to specific keys that correspond to even inline values (GQ, for example). Can be very expensive. Additionally, all int[] are converted inline into List<Integer> for convenience.
    
    Parameters:
    key -
    
    Returns:
  - hasAnyAttribute
```
public boolean hasAnyAttribute(java.lang.String key)
```
  - sortedString
```
protected static <T extends java.lang.Comparable<T>,V> java.lang.String sortedString(java.util.Map<T,V> c)
```
    a utility method for generating sorted strings from a map key set.
    
    Type Parameters:
    T - the key type
    V - the value type
    Parameters:
    c - the map
    
    Returns:
    a sting, enclosed in {}, with comma seperated key value pairs in order of the keys
  - toStringIfExists
```
protected static final java.lang.String toStringIfExists(java.lang.String name,
                                int v)
```
    Returns a display name for field name with value v if this isn't -1. Otherwise returns ""
    
    Parameters:
    name - of the field ("AD")
    v - the value of the field, or -1 if missing
    
    Returns:
    a non-null string for display if the field is not missing
  - toStringIfExists
```
protected static final java.lang.String toStringIfExists(java.lang.String name,
                                java.lang.String v)
```
    Returns a display name for field name with String value v if this isn't null. Otherwise returns ""
    
    Parameters:
    name - of the field ("FT")
    v - the value of the field, or null if missing
    
    Returns:
    a non-null string for display if the field is not missing
  - toStringIfExists
```
protected static final java.lang.String toStringIfExists(java.lang.String name,
                                int[] vs)
```
    Returns a display name for field name with values vs if this isn't null. Otherwise returns ""
    
    Parameters:
    name - of the field ("AD")
    vs - the value of the field, or null if missing
    
    Returns:
    a non-null string for display if the field is not missing
  - hasForbiddenKey
```
protected static final boolean hasForbiddenKey(java.util.Map<java.lang.String,java.lang.Object> attributes)
```
    Does the attribute map have a mapping involving a forbidden key (i.e., one that's managed inline by this Genotypes object?
    
    Parameters:
    attributes - the extended attributes key
    
    Returns:
  - isForbiddenKey
```
protected static final boolean isForbiddenKey(java.lang.String key)
```

Class Genotype

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

PRIMARY_KEYS

PHASED_ALLELE_SEPARATOR

UNPHASED_ALLELE_SEPARATOR

Constructor Detail

Genotype

Method Detail

getAlleles

countAllele

getAllele

isPhased

getPloidy

getDP

getAD

getSampleName

getGQ

hasPL

hasAD

hasGQ

hasDP

getType

determineType

isHom

isHomRef

isHomVar

isHet

isHetNonRef

isNoCall

isCalled

isMixed

isAvailable

hasLikelihoods

getLikelihoodsString

getLikelihoods

isNonInformative

getPL

getGenotypeString

getGenotypeString

getAlleleStrings

toString

toBriefString

compareTo

sameGenotype

sameGenotype

getExtendedAttributes

hasExtendedAttribute

getExtendedAttribute

getExtendedAttribute

getFilters

isFiltered

hasLog10PError

getLog10PError

getPhredScaledQual

getAttributeAsString

getAttributeAsInt

getAttributeAsDouble

getAnyAttribute

hasAnyAttribute

sortedString

toStringIfExists

toStringIfExists

toStringIfExists

hasForbiddenKey

isForbiddenKey