Package org.snpeff.vcf
Class VcfHeaderInfo
java.lang.Object
org.snpeff.vcf.VcfHeaderEntry
org.snpeff.vcf.VcfHeaderInfo
- All Implemented Interfaces:
Serializable
- Direct Known Subclasses:
VcfHeaderFormat
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=invalid input: '<'ID=ID,Number=number,Type=type,Description=description>
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
- See Also:
-
Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
Number of values in an INFO field. -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String
protected boolean
protected int
protected VcfHeaderInfo.VcfInfoNumber
protected VcfInfoType
Fields inherited from class org.snpeff.vcf.VcfHeaderEntry
id, line
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Constructor Summary
ConstructorsConstructorDescriptionVcfHeaderInfo
(String line) Constructor using a "##INFO" line from a VCF fileVcfHeaderInfo
(String id, VcfInfoType vcfInfoType, String number, String description) VcfHeaderInfo
(VcfHeaderInfo header) -
Method Summary
Modifier and TypeMethodDescriptionint
boolean
boolean
isInfo()
boolean
boolean
boolean
boolean
boolean
void
setImplicit
(boolean implicit) void
setNumber
(int number) void
void
setVcfInfoNumber
(VcfHeaderInfo.VcfInfoNumber vcfInfoNumber) void
setVcfInfoType
(VcfInfoType vcfInfoType) toString()
Methods inherited from class org.snpeff.vcf.VcfHeaderEntry
factory, getId, isFormat, setId
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Field Details
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number
protected int number -
implicit
protected boolean implicit -
vcfInfoNumber
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vcfInfoType
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description
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Constructor Details
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VcfHeaderInfo
Constructor using a "##INFO" line from a VCF file -
VcfHeaderInfo
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VcfHeaderInfo
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Method Details
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getDescription
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getNumber
public int getNumber() -
getNumberString
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getVcfInfoNumber
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getVcfInfoType
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isImplicit
public boolean isImplicit() -
isInfo
public boolean isInfo()- Overrides:
isInfo
in classVcfHeaderEntry
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isNumberAllAlleles
public boolean isNumberAllAlleles() -
isNumberNumber
public boolean isNumberNumber() -
isNumberOnePerAllele
public boolean isNumberOnePerAllele() -
isNumberOnePerGenotype
public boolean isNumberOnePerGenotype() -
isNumberPerAllele
public boolean isNumberPerAllele() -
setImplicit
public void setImplicit(boolean implicit) -
setNumber
public void setNumber(int number) -
setNumber
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setVcfInfoNumber
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setVcfInfoType
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toString
- Overrides:
toString
in classVcfHeaderEntry
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