Package org.snpeff.vcf
Class VcfHeaderInfo
- java.lang.Object
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- org.snpeff.vcf.VcfHeaderEntry
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- org.snpeff.vcf.VcfHeaderInfo
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- Direct Known Subclasses:
VcfHeaderFormat
public class VcfHeaderInfo extends VcfHeaderEntry
Represents a info elements in a VCF file References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 INFO fields should be described as follows (all keys are required): ##INFO=Possible Types for INFO fields are: Integer, Float, Flag, Character, and String. The Number entry is an Integer that describes the number of values that can be included with the INFO field. For example, if the INFO field contains a single number, then this value should be 1; if the INFO field describes a pair of numbers, then this value should be 2 and so on. If the field has one value per alternate allele then this value should be 'A'; if the field has one value for each possible genotype (more relevant to the FORMAT tags) then this value should be 'G'. If the number of possible values varies, is unknown, or is unbounded, then this value should be '.'. The 'Flag' type indicates that the INFO field does not contain a Value entry, and hence the Number should be 0 in this case. The Description value must be surrounded by double-quotes. Double-quote character can be escaped with backslash (\") and backslash as \\. - Author:
- pablocingolani
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
VcfHeaderInfo.VcfInfoNumber
Number of values in an INFO field.
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
description
protected boolean
implicit
protected int
number
protected VcfHeaderInfo.VcfInfoNumber
vcfInfoNumber
protected VcfInfoType
vcfInfoType
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Fields inherited from class org.snpeff.vcf.VcfHeaderEntry
id, line
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Constructor Summary
Constructors Constructor Description VcfHeaderInfo(java.lang.String line)
Constructor using a "##INFO" line from a VCF fileVcfHeaderInfo(java.lang.String id, VcfInfoType vcfInfoType, java.lang.String number, java.lang.String description)
VcfHeaderInfo(VcfHeaderInfo header)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getDescription()
int
getNumber()
VcfHeaderInfo.VcfInfoNumber
getVcfInfoNumber()
VcfInfoType
getVcfInfoType()
boolean
isImplicit()
boolean
isInfo()
boolean
isNumberAllAlleles()
boolean
isNumberNumber()
boolean
isNumberOnePerAllele()
boolean
isNumberOnePerGenotype()
boolean
isNumberPerAllele()
void
setImplicit(boolean implicit)
void
setNumber(int number)
void
setNumber(java.lang.String number)
void
setVcfInfoNumber(VcfHeaderInfo.VcfInfoNumber vcfInfoNumber)
void
setVcfInfoType(VcfInfoType vcfInfoType)
java.lang.String
toString()
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Methods inherited from class org.snpeff.vcf.VcfHeaderEntry
factory, getId, isFormat, setId
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Field Detail
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number
protected int number
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implicit
protected boolean implicit
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vcfInfoNumber
protected VcfHeaderInfo.VcfInfoNumber vcfInfoNumber
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vcfInfoType
protected VcfInfoType vcfInfoType
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description
protected java.lang.String description
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Constructor Detail
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VcfHeaderInfo
public VcfHeaderInfo(java.lang.String line)
Constructor using a "##INFO" line from a VCF file
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VcfHeaderInfo
public VcfHeaderInfo(java.lang.String id, VcfInfoType vcfInfoType, java.lang.String number, java.lang.String description)
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VcfHeaderInfo
public VcfHeaderInfo(VcfHeaderInfo header)
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Method Detail
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getDescription
public java.lang.String getDescription()
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getNumber
public int getNumber()
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getVcfInfoNumber
public VcfHeaderInfo.VcfInfoNumber getVcfInfoNumber()
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getVcfInfoType
public VcfInfoType getVcfInfoType()
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isImplicit
public boolean isImplicit()
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isInfo
public boolean isInfo()
- Overrides:
isInfo
in classVcfHeaderEntry
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isNumberAllAlleles
public boolean isNumberAllAlleles()
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isNumberNumber
public boolean isNumberNumber()
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isNumberOnePerAllele
public boolean isNumberOnePerAllele()
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isNumberOnePerGenotype
public boolean isNumberOnePerGenotype()
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isNumberPerAllele
public boolean isNumberPerAllele()
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setImplicit
public void setImplicit(boolean implicit)
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setNumber
public void setNumber(int number)
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setNumber
public void setNumber(java.lang.String number)
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setVcfInfoNumber
public void setVcfInfoNumber(VcfHeaderInfo.VcfInfoNumber vcfInfoNumber)
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setVcfInfoType
public void setVcfInfoType(VcfInfoType vcfInfoType)
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toString
public java.lang.String toString()
- Overrides:
toString
in classVcfHeaderEntry
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