org.nmdp.ngs.variant.vcf

Class VcfRecord

java.lang.Object

org.nmdp.ngs.variant.vcf.VcfRecord

@Immutable
public final class VcfRecord
extends Object

VCF record.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VcfRecord.Builder VCF record builder.

Method Summary

Methods

Modifier and Type	Method and Description
static VcfRecord.Builder	builder() Create and return a new VCF record builder.
String[]	getAlt() Return the alternate alleles for this VCF record.
String	getChrom() Return the chromosome for this VCF record.
String[]	getFilter() Return the filter for this VCF record.
String[]	getFormat() Return the format for this VCF record.
Map<String,VcfGenotype>	getGenotypes() Return the genotypes keyed by sample id for this VCF record.
String[]	getId() Return the array of ids for this VCF record.
com.google.common.collect.ListMultimap<String,String>	getInfo() Return the INFO key-value(s) pairs for this VCF record.
long	getLineNumber() Return the line number for this VCF record.
long	getPos() Return the position for this VCF record.
double	getQual() Return the QUAL score for this VCF record.
String	getRef() Return the reference allele for this VCF record.

Methods inherited from class java.lang.Object

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

Method Detail

getLineNumber

public long getLineNumber()

Return the line number for this VCF record.

Returns:

the line number for this VCF record

getChrom

public String getChrom()

Return the chromosome for this VCF record.

Returns:

the chromosome for this VCF record

getPos

public long getPos()

Return the position for this VCF record.

Returns:

the position for this VCF record

getId

public String[] getId()

Return the array of ids for this VCF record.

Returns:

the array of ids for this VCF record

getRef

public String getRef()

Return the reference allele for this VCF record.

Returns:

the reference allele for this VCF record

getAlt

public String[] getAlt()

Return the alternate alleles for this VCF record.

Returns:

the alternate alleles for this VCF record

getQual

public double getQual()

Return the QUAL score for this VCF record.

Returns:

the QUAL score for this VCF record

getFilter

public String[] getFilter()

Return the filter for this VCF record.

Returns:

the filter for this VCF record

getInfo

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

Return the INFO key-value(s) pairs for this VCF record.

Returns:

the INFO key-value(s) pairs for this VCF record

getFormat

public String[] getFormat()

Return the format for this VCF record.

Returns:

the format for this VCF record

getGenotypes

public Map<String,VcfGenotype> getGenotypes()

Return the genotypes keyed by sample id for this VCF record.

Returns:

the genotypes keyed by sample id for this VCF record

builder

public static VcfRecord.Builder builder()

Create and return a new VCF record builder.

Returns:

a new VCF record builder