Package org.pharmgkb.parser.vcf.model

Class VcfPosition

java.lang.Object

org.pharmgkb.parser.vcf.model.VcfPosition

public class VcfPosition
extends Object

This class contains the basic data (the first 9 columns) for a VCF position line.

 0 - CHROM
 1 - POS
 2 - ID
 3 - REF
 4 - ALT
 5 - QUAL
 6 - FILTER
 7 - INFO
 8 - FORMAT
 

Constructor Summary

Constructors

Constructor	Description
VcfPosition(String chromosome, long position, String refBases, BigDecimal quality)
VcfPosition(String chr, long pos, List<String> ids, String ref, List<String> altBases, BigDecimal qual, List<String> filter, com.google.common.collect.ListMultimap<String,String> info, List<String> format)

Method Summary

Modifier and Type	Method	Description
String	getAllele(int index)	Gets the allele at the given index from a list of containing refBases + altBases.
List<String>	getAltBases()	Gets the alternate base(s) for this position.
String	getChromosome()	Gets an identifier from the reference genome or an angle-bracketed ID String ("<ID>") pointing to a contig in the assembly file.
List<String>	getFilters()	Returns a list of filters this position failed, if any.
List<String>	getFormat()
List<String>	getIds()	Gets the list of unique identifiers for this position.
com.google.common.collect.ListMultimap<String,String>	getInfo()	Gets all INFO fields for every key.
List<String>	getInfo(String id)	Get INFO metadata with the specified ID.
<T> T	getInfo(ReservedInfoProperty key)	Returns the value for the reserved property as the type specified by both ReservedInfoProperty.getType() and ReservedInfoProperty.isList().
Set<String>	getInfoKeys()
long	getPosition()
BigDecimal	getQuality()
String	getRef()	Gets the reference base(s) for this position.
boolean	hasInfo(String id)	Checks if there is INFO metadata with the specified ID.
boolean	hasInfo(ReservedInfoProperty key)	Checks if there is INFO metadata with the specified ID.
boolean	isPassingAllFilters()
void	setChromosome(String chromosome)
void	setPosition(long position)
void	setQuality(BigDecimal quality)
void	setRef(String ref)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

VcfPosition

public VcfPosition(@Nonnull
 String chr,
 long pos,
 @Nullable
 List<String> ids,
 @Nonnull
 String ref,
 @Nullable
 List<String> altBases,
 @Nullable
 BigDecimal qual,
 @Nullable
 List<String> filter,
 @Nullable
 com.google.common.collect.ListMultimap<String,String> info,
 @Nullable
 List<String> format)

VcfPosition

public VcfPosition(@Nonnull
 String chromosome,
 long position,
 @Nonnull
 String refBases,
 @Nonnull
 BigDecimal quality)

Method Details

getChromosome

@Nonnull
public String getChromosome()

Gets an identifier from the reference genome or an angle-bracketed ID String ("<ID>") pointing to a contig in the assembly file.

setChromosome

public void setChromosome(@Nonnull
 String chromosome)

setRef

public void setRef(@Nonnull
 String ref)

getPosition

public long getPosition()

setPosition

public void setPosition(long position)

getIds

@Nonnull
public List<String> getIds()

Gets the list of unique identifiers for this position.

getRef

@Nonnull
public String getRef()

Gets the reference base(s) for this position. Each base must be an A, C, G, T, or N.

getAltBases

@Nonnull
public List<String> getAltBases()

Gets the alternate base(s) for this position. Each base must be an A, C, G, T, N or * unless it's an angle-bracketed ID string ("<ID>").

ID strings should reference a specific ALT metadata (obtainable via VcfMetadata.getAlt(java.lang.String)).

getAllele

@Nonnull
public String getAllele(int index)

Gets the allele at the given index from a list of containing refBases + altBases.

Throws:

IndexOutOfBoundsException - if index is out of range

getQuality

@Nullable
public BigDecimal getQuality()

setQuality

public void setQuality(@Nullable
 BigDecimal quality)

isPassingAllFilters

public boolean isPassingAllFilters()

getFilters

@Nonnull
public List<String> getFilters()

Returns a list of filters this position failed, if any.

getInfo

@Nonnull
public com.google.common.collect.ListMultimap<String,String> getInfo()

Gets all INFO fields for every key.

getInfo

@Nullable
public List<String> getInfo(@Nonnull
 String id)

Get INFO metadata with the specified ID.

Returns:

list of values or null if there is no INFO metadata for the specified id

getInfo

@Nullable
public <T> T getInfo(@Nonnull
 ReservedInfoProperty key)

Returns the value for the reserved property as the type specified by both ReservedInfoProperty.getType() and ReservedInfoProperty.isList().

Note that this method does NOT always return a list.

For example:

   BigDecimal bq = vcfPosition.getInfoConverted(ReservedInfoProperty.BaseQuality);
 
 

Type Parameters:

T - The type specified by ReservedInfoProperty.getType() if ReservedInfoProperty.isList() is false; otherwise List<V> where V is the type specified by ReservedInfoProperty.getType().

hasInfo

public boolean hasInfo(@Nonnull
 String id)

Checks if there is INFO metadata with the specified ID.

hasInfo

public boolean hasInfo(@Nonnull
 ReservedInfoProperty key)

Checks if there is INFO metadata with the specified ID.

getFormat

@Nonnull
public List<String> getFormat()

getInfoKeys

@Nonnull
public Set<String> getInfoKeys()