org.pharmgkb.parser.vcf.model

Class VcfPosition

java.lang.Object

org.pharmgkb.parser.vcf.model.VcfPosition

public class VcfPosition
extends java.lang.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 and Description
VcfPosition(java.lang.String chr, long pos, java.util.List<java.lang.String> ids, java.lang.String ref, java.util.List<java.lang.String> altBases, java.math.BigDecimal qual, java.util.List<java.lang.String> filter, com.google.common.collect.ListMultimap<java.lang.String,java.lang.String> info, java.util.List<java.lang.String> format)
VcfPosition(java.lang.String chromosome, long position, java.lang.String refBases, java.math.BigDecimal quality)

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfPosition

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

VcfPosition

public VcfPosition(@Nonnull
                   java.lang.String chromosome,
                   long position,
                   @Nonnull
                   java.lang.String refBases,
                   @Nonnull
                   java.math.BigDecimal quality)

Method Detail

getChromosome

@Nonnull
public java.lang.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
                          java.lang.String chromosome)

setRef

public void setRef(@Nonnull
                   java.lang.String ref)

getPosition

public long getPosition()

setPosition

public void setPosition(long position)

getIds

@Nonnull
public java.util.List<java.lang.String> getIds()

Gets the list of unique identifiers for this position.

getRef

@Nonnull
public java.lang.String getRef()

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

getAltBases

@Nonnull
public java.util.List<java.lang.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 java.lang.String getAllele(int index)

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

Throws:

java.lang.IndexOutOfBoundsException - if index is out of range

getQuality

@Nullable
public java.math.BigDecimal getQuality()

setQuality

public void setQuality(@Nullable
                       java.math.BigDecimal quality)

isPassingAllFilters

public boolean isPassingAllFilters()

getFilters

@Nonnull
public java.util.List<java.lang.String> getFilters()

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

getInfo

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

Gets all INFO fields for every key.

getInfo

@Nullable
public java.util.List<java.lang.String> getInfo(@Nonnull
                                                           java.lang.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
                       java.lang.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 java.util.List<java.lang.String> getFormat()

getInfoKeys

@Nonnull
public java.util.Set<java.lang.String> getInfoKeys()