org.molgenis.vcf.meta

Class VcfMeta

java.lang.Object

org.molgenis.vcf.meta.VcfMeta

public class VcfMeta
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	COL_ALT_IDX
static int	COL_CHROM_IDX
static int	COL_FILTER_IDX
static int	COL_FORMAT_IDX
static int	COL_ID_IDX
static int	COL_INFO_IDX
static int	COL_POS_IDX
static int	COL_QUAL_IDX
static int	COL_REF_IDX

Constructor Summary

Constructors

Constructor and Description
VcfMeta()

Method Summary

Modifier and Type	Method and Description
void	add(String key, String value)
void	addAltMeta(VcfMetaAlt vcfMetaAlt)
void	addContigMeta(VcfMetaContig vcfMetaContig)
void	addFilterMeta(VcfMetaFilter vcfMetaFilter)
void	addFormatMeta(VcfMetaFormat vcfMetaFormat)
void	addInfoMeta(VcfMetaInfo vcfMetaInfo)
void	addPedigreeMeta(VcfMetaPedigree vcfMetaPedigree)
void	addSampleMeta(VcfMetaSample vcfMetaSample)
String	get(String key)
Iterable<VcfMetaAlt>	getAltMeta()
VcfMetaAlt	getAltMeta(String id)
String[]	getColNames()
Iterable<VcfMetaContig>	getContigMeta()
VcfMetaContig	getContigMeta(String id)
String	getFileFormat()
Iterable<VcfMetaFilter>	getFilterMeta()
VcfMetaFilter	getFilterMeta(String id)
Iterable<VcfMetaFormat>	getFormatMeta()
VcfMetaFormat	getFormatMeta(String id)
Iterable<VcfMetaInfo>	getInfoMeta()
VcfMetaInfo	getInfoMeta(String id)
Map<String,String>	getMeta()
Iterable<VcfMetaPedigree>	getPedigreeMeta()
Iterable<VcfMetaSample>	getSampleMeta()
VcfMetaSample	getSampleMeta(String id)
String	getSampleName(int nr)
Iterable<String>	getSampleNames()
void	setColNames(String[] colNames)
void	setVcfMetaSamples(Map<String,VcfMetaSample> vcfMetaSamples)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

COL_CHROM_IDX

public static final int COL_CHROM_IDX

See Also:

Constant Field Values

COL_POS_IDX

public static final int COL_POS_IDX

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Constant Field Values

COL_ID_IDX

public static final int COL_ID_IDX

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Constant Field Values

COL_REF_IDX

public static final int COL_REF_IDX

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Constant Field Values

COL_ALT_IDX

public static final int COL_ALT_IDX

See Also:

Constant Field Values

COL_QUAL_IDX

public static final int COL_QUAL_IDX

See Also:

Constant Field Values

COL_FILTER_IDX

public static final int COL_FILTER_IDX

See Also:

Constant Field Values

COL_INFO_IDX

public static final int COL_INFO_IDX

See Also:

Constant Field Values

COL_FORMAT_IDX

public static final int COL_FORMAT_IDX

See Also:

Constant Field Values

Constructor Detail

VcfMeta

public VcfMeta()

Method Detail

getMeta

public Map<String,String> getMeta()

getFileFormat

public String getFileFormat()

add

public void add(String key,
                String value)

get

public String get(String key)

setColNames

public void setColNames(String[] colNames)

getColNames

public String[] getColNames()

getSampleName

public String getSampleName(int nr)

getSampleNames

public Iterable<String> getSampleNames()

addAltMeta

public void addAltMeta(VcfMetaAlt vcfMetaAlt)

getAltMeta

public Iterable<VcfMetaAlt> getAltMeta()

getAltMeta

public VcfMetaAlt getAltMeta(String id)

addContigMeta

public void addContigMeta(VcfMetaContig vcfMetaContig)

getContigMeta

public Iterable<VcfMetaContig> getContigMeta()

getContigMeta

public VcfMetaContig getContigMeta(String id)

addFilterMeta

public void addFilterMeta(VcfMetaFilter vcfMetaFilter)

getFilterMeta

public Iterable<VcfMetaFilter> getFilterMeta()

getFilterMeta

public VcfMetaFilter getFilterMeta(String id)

addFormatMeta

public void addFormatMeta(VcfMetaFormat vcfMetaFormat)

getFormatMeta

public Iterable<VcfMetaFormat> getFormatMeta()

getFormatMeta

public VcfMetaFormat getFormatMeta(String id)

addInfoMeta

public void addInfoMeta(VcfMetaInfo vcfMetaInfo)

getInfoMeta

public Iterable<VcfMetaInfo> getInfoMeta()

getInfoMeta

public VcfMetaInfo getInfoMeta(String id)

addPedigreeMeta

public void addPedigreeMeta(VcfMetaPedigree vcfMetaPedigree)

getPedigreeMeta

public Iterable<VcfMetaPedigree> getPedigreeMeta()

setVcfMetaSamples

public void setVcfMetaSamples(Map<String,VcfMetaSample> vcfMetaSamples)

addSampleMeta

public void addSampleMeta(VcfMetaSample vcfMetaSample)

getSampleMeta

public Iterable<VcfMetaSample> getSampleMeta()

getSampleMeta

public VcfMetaSample getSampleMeta(String id)

toString

public String toString()

Overrides:

toString in class Object