org.brapi.v2.model.geno

Class BrAPIVariant

java.lang.Object

org.brapi.v2.model.geno.BrAPIVariant

public class BrAPIVariant
extends Object

A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a SNP or an insertion. Variants belong to a `VariantSet`. This is equivalent to a row in VCF.

Constructor Summary

Constructors

Constructor and Description
BrAPIVariant()

Method Summary

Modifier and Type	Method and Description
BrAPIVariant	addAlternateBasesItem(String alternateBasesItem)
BrAPIVariant	addCiendItem(Integer ciendItem)
BrAPIVariant	addCiposItem(Integer ciposItem)
BrAPIVariant	addFiltersFailedItem(String filtersFailedItem)
BrAPIVariant	additionalInfo(com.google.gson.JsonObject additionalInfo)
BrAPIVariant	addVariantNamesItem(String variantNamesItem)
BrAPIVariant	addVariantSetDbIdItem(String variantSetDbIdItem)
BrAPIVariant	alternateBases(List<String> alternateBases)
BrAPIVariant	ciend(List<Integer> ciend)
BrAPIVariant	cipos(List<Integer> cipos)
BrAPIVariant	created(OffsetDateTime created)
BrAPIVariant	end(Integer end)
boolean	equals(Object o)
BrAPIVariant	externalReferences(List<BrAPIExternalReference> externalReferences)
BrAPIVariant	filtersApplied(Boolean filtersApplied)
BrAPIVariant	filtersFailed(List<String> filtersFailed)
BrAPIVariant	filtersPassed(Boolean filtersPassed)
com.google.gson.JsonObject	getAdditionalInfo() Additional arbitrary info
List<String>	getAlternate_bases() Deprecated.
List<String>	getAlternateBases() The bases that appear instead of the reference bases.
List<Integer>	getCiend() Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen).
List<Integer>	getCipos() In the case of structural variants, start and end of the variant may not be known with an exact base position.
@Valid OffsetDateTime	getCreated() The timestamp when this variant was created.
Integer	getEnd() This field is optional and may be ignored if there is no relevant map or reference to be associated with.
@Valid List<BrAPIExternalReference>	getExternalReferences() Get externalReferences
List<String>	getFiltersFailed() Zero or more filters that failed for this variant.
String	getReferenceBases() The reference bases for this variant.
String	getReferenceDbId() The unique identifier for a Reference
String	getReferenceName() The reference on which this variant occurs.
String	getReferenceSetDbId() The unique identifier for a ReferenceSet
String	getReferenceSetName() The human readable name of the ReferenceSet
Integer	getStart() This field is optional and may be ignored if there is no relevant map or reference to be associated with.
Integer	getSvlen() Length of the - if labeled as such in variant_type - structural variation.
@Valid OffsetDateTime	getUpdated() The time at which this variant was last updated.
String	getVariantDbId() The variant ID.
List<String>	getVariantNames() Names for the variant, for example a RefSNP ID.
List<String>	getVariantSetDbId() An array of `VariantSet` IDs this variant belongs to.
String	getVariantType() The \"variant_type\" is used to denote e.g.
int	hashCode()
Boolean	isFiltersApplied() True if filters were applied for this variant.
Boolean	isFiltersPassed() True if all filters for this variant passed.
BrAPIVariant	putAdditionalInfoItem(String key, Object additionalInfoItem)
BrAPIVariant	referenceBases(String referenceBases)
BrAPIVariant	referenceDbId(String referenceDbId)
BrAPIVariant	referenceName(String referenceName)
BrAPIVariant	referenceSetDbId(String referenceSetDbId)
BrAPIVariant	referenceSetName(String referenceSetName)
void	setAdditionalInfo(com.google.gson.JsonObject additionalInfo)
void	setAlternateBases(List<String> alternateBases)
void	setCiend(List<Integer> ciend)
void	setCipos(List<Integer> cipos)
void	setCreated(OffsetDateTime created)
void	setEnd(Integer end)
void	setExternalReferences(List<BrAPIExternalReference> externalReferences)
void	setFiltersApplied(Boolean filtersApplied)
void	setFiltersFailed(List<String> filtersFailed)
void	setFiltersPassed(Boolean filtersPassed)
void	setReferenceBases(String referenceBases)
void	setReferenceDbId(String referenceDbId)
void	setReferenceName(String referenceName)
void	setReferenceSetDbId(String referenceSetDbId)
void	setReferenceSetName(String referenceSetName)
void	setStart(Integer start)
void	setSvlen(Integer svlen)
void	setUpdated(OffsetDateTime updated)
void	setVariantDbId(String variantDbId)
void	setVariantNames(List<String> variantNames)
void	setVariantSetDbId(List<String> variantSetDbId)
void	setVariantType(String variantType)
BrAPIVariant	start(Integer start)
BrAPIVariant	svlen(Integer svlen)
String	toString()
BrAPIVariant	updated(OffsetDateTime updated)
BrAPIVariant	variantDbId(String variantDbId)
BrAPIVariant	variantNames(List<String> variantNames)
BrAPIVariant	variantSetDbId(List<String> variantSetDbId)
BrAPIVariant	variantType(String variantType)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BrAPIVariant

public BrAPIVariant()

Method Detail

additionalInfo

public BrAPIVariant additionalInfo(com.google.gson.JsonObject additionalInfo)

putAdditionalInfoItem

public BrAPIVariant putAdditionalInfoItem(String key,
                                          Object additionalInfoItem)

getAdditionalInfo

public com.google.gson.JsonObject getAdditionalInfo()

Additional arbitrary info

Returns:

additionalInfo

setAdditionalInfo

public void setAdditionalInfo(com.google.gson.JsonObject additionalInfo)

alternateBases

public BrAPIVariant alternateBases(List<String> alternateBases)

addAlternateBasesItem

public BrAPIVariant addAlternateBasesItem(String alternateBasesItem)

getAlternate_bases

@Deprecated
public List<String> getAlternate_bases()

Deprecated.

Deprecated, use getAlternateBases

Returns:

getAlternateBases

public List<String> getAlternateBases()

The bases that appear instead of the reference bases. Multiple alternate alleles are possible.

Returns:

alternateBases

setAlternateBases

public void setAlternateBases(List<String> alternateBases)

ciend

public BrAPIVariant ciend(List<Integer> ciend)

addCiendItem

public BrAPIVariant addCiendItem(Integer ciendItem)

getCiend

public List<Integer> getCiend()

Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen).

Returns:

ciend

setCiend

public void setCiend(List<Integer> ciend)

cipos

public BrAPIVariant cipos(List<Integer> cipos)

addCiposItem

public BrAPIVariant addCiposItem(Integer ciposItem)

getCipos

public List<Integer> getCipos()

In the case of structural variants, start and end of the variant may not be known with an exact base position. \"cipos\" provides an interval with high confidence for the start position. The interval is provided by 0 or 2 signed integers which are added to the start position. Based on the use in VCF v4.2

Returns:

cipos

setCipos

public void setCipos(List<Integer> cipos)

created

public BrAPIVariant created(OffsetDateTime created)

getCreated

@Valid
public @Valid OffsetDateTime getCreated()

The timestamp when this variant was created.

Returns:

created

setCreated

public void setCreated(OffsetDateTime created)

end

public BrAPIVariant end(Integer end)

getEnd

public Integer getEnd()

This field is optional and may be ignored if there is no relevant map or reference to be associated with. The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated by `start + referenceBases.length`.

Returns:

end

setEnd

public void setEnd(Integer end)

externalReferences

public BrAPIVariant externalReferences(List<BrAPIExternalReference> externalReferences)

getExternalReferences

@Valid
public @Valid List<BrAPIExternalReference> getExternalReferences()

Get externalReferences

Returns:

externalReferences

setExternalReferences

public void setExternalReferences(List<BrAPIExternalReference> externalReferences)

filtersApplied

public BrAPIVariant filtersApplied(Boolean filtersApplied)

isFiltersApplied

public Boolean isFiltersApplied()

True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value.

Returns:

filtersApplied

setFiltersApplied

public void setFiltersApplied(Boolean filtersApplied)

filtersFailed

public BrAPIVariant filtersFailed(List<String> filtersFailed)

addFiltersFailedItem

public BrAPIVariant addFiltersFailedItem(String filtersFailedItem)

getFiltersFailed

public List<String> getFiltersFailed()

Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record.

Returns:

filtersFailed

setFiltersFailed

public void setFiltersFailed(List<String> filtersFailed)

filtersPassed

public BrAPIVariant filtersPassed(Boolean filtersPassed)

isFiltersPassed

public Boolean isFiltersPassed()

True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS.

Returns:

filtersPassed

setFiltersPassed

public void setFiltersPassed(Boolean filtersPassed)

referenceBases

public BrAPIVariant referenceBases(String referenceBases)

getReferenceBases

public String getReferenceBases()

The reference bases for this variant. They start at the given start position.

Returns:

referenceBases

setReferenceBases

public void setReferenceBases(String referenceBases)

referenceDbId

public BrAPIVariant referenceDbId(String referenceDbId)

getReferenceDbId

public String getReferenceDbId()

The unique identifier for a Reference

Returns:

referenceDbId

setReferenceDbId

public void setReferenceDbId(String referenceDbId)

referenceName

public BrAPIVariant referenceName(String referenceName)

getReferenceName

public String getReferenceName()

The reference on which this variant occurs. (e.g. `chr_20` or `X`)

Returns:

referenceName

setReferenceName

public void setReferenceName(String referenceName)

referenceSetDbId

public BrAPIVariant referenceSetDbId(String referenceSetDbId)

getReferenceSetDbId

public String getReferenceSetDbId()

The unique identifier for a ReferenceSet

Returns:

referenceSetDbId

setReferenceSetDbId

public void setReferenceSetDbId(String referenceSetDbId)

referenceSetName

public BrAPIVariant referenceSetName(String referenceSetName)

getReferenceSetName

public String getReferenceSetName()

The human readable name of the ReferenceSet

Returns:

referenceSetName

setReferenceSetName

public void setReferenceSetName(String referenceSetName)

start

public BrAPIVariant start(Integer start)

getStart

public Integer getStart()

This field is optional and may be ignored if there is no relevant map or reference to be associated with. The start position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning the join of circular genomes are represented as two variants one on each side of the join (position 0).

Returns:

start

setStart

public void setStart(Integer start)

svlen

public BrAPIVariant svlen(Integer svlen)

getSvlen

public Integer getSvlen()

Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2

Returns:

svlen

setSvlen

public void setSvlen(Integer svlen)

updated

public BrAPIVariant updated(OffsetDateTime updated)

getUpdated

@Valid
public @Valid OffsetDateTime getUpdated()

The time at which this variant was last updated.

Returns:

updated

setUpdated

public void setUpdated(OffsetDateTime updated)

variantDbId

public BrAPIVariant variantDbId(String variantDbId)

getVariantDbId

public String getVariantDbId()

The variant ID.

Returns:

variantDbId

setVariantDbId

public void setVariantDbId(String variantDbId)

variantNames

public BrAPIVariant variantNames(List<String> variantNames)

addVariantNamesItem

public BrAPIVariant addVariantNamesItem(String variantNamesItem)

getVariantNames

public List<String> getVariantNames()

Names for the variant, for example a RefSNP ID.

Returns:

variantNames

setVariantNames

public void setVariantNames(List<String> variantNames)

variantSetDbId

public BrAPIVariant variantSetDbId(List<String> variantSetDbId)

addVariantSetDbIdItem

public BrAPIVariant addVariantSetDbIdItem(String variantSetDbIdItem)

getVariantSetDbId

public List<String> getVariantSetDbId()

An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted.

Returns:

variantSetDbId

setVariantSetDbId

public void setVariantSetDbId(List<String> variantSetDbId)

variantType

public BrAPIVariant variantType(String variantType)

getVariantType

public String getVariantType()

The \"variant_type\" is used to denote e.g. structural variants. Examples: DUP : duplication of sequence following \"start\" DEL : deletion of sequence following \"start\"

Returns:

variantType

setVariantType

public void setVariantType(String variantType)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object