Package org.snpeff.vcf
Class VcfGenotype
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- org.snpeff.vcf.VcfGenotype
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public class VcfGenotype extends java.lang.Object
A VCF genotype field There is one genotype per sample in each VCF entry- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
GT_FIELD_ALLELIC_DEPTH_OF_COVERAGE
static java.lang.String
GT_FIELD_DEPTH_OF_COVERAGE
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Constructor Summary
Constructors Constructor Description VcfGenotype(VcfEntry vcfEntry, java.lang.String format, java.lang.String values)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(java.lang.String name, java.lang.String value)
Add a name=value pair WARNING: This method does NOT change the FORMAT field.int
depth()
Depth of coveragejava.lang.String
get(java.lang.String fieldName)
Get a genotype fieldint[]
getGenotype()
Get genotype numbers as an array E.g.java.lang.String
getGenotype(int idx)
Get genotype string by index WARNING: If the genotype is missing, it returns an empty string.int
getGenotypeCode()
Return as a genotype SNP code: -1: if missing data of more than one ALT 0: if aa (0/0) 1: if Aa (0/1 or 1/0) 2: if AA (1/1) WARNING: In multi-allelic case, any non-ref is treated as ALTint
getGenotypeCodeIgnoreMissing()
Return as a genotype SNP code: 0: if aa (0/0) or any missing value 1: if Aa (0/1 or 1/0) 2: if AA (1/1)java.lang.String
getGenotypeStr()
Return genotypes as string (e.g.VcfEntry
getVcfEntry()
boolean
isHeterozygous()
Is the most likely genotype heterozygous?boolean
isHomozygous()
Is this genotype homozygous? (either REF or ALT)boolean
isHomozygousAlt()
Is this genotype homozygous ALT?boolean
isMissing()
Is genotpye missing (e.g.boolean
isPhased()
boolean
isRef()
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)boolean
isVariant()
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)int
plodity()
Genotype plodity (i.e.void
set(java.lang.String gtFieldName, java.lang.String gtValue)
Set a genotype field valuevoid
setGenotype(java.lang.String gtValue)
Set genotype valuejava.lang.String
toString()
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Field Detail
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GT_FIELD_DEPTH_OF_COVERAGE
public static final java.lang.String GT_FIELD_DEPTH_OF_COVERAGE
- See Also:
- Constant Field Values
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GT_FIELD_ALLELIC_DEPTH_OF_COVERAGE
public static final java.lang.String GT_FIELD_ALLELIC_DEPTH_OF_COVERAGE
- See Also:
- Constant Field Values
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Constructor Detail
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VcfGenotype
public VcfGenotype(VcfEntry vcfEntry, java.lang.String format, java.lang.String values)
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Method Detail
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add
public void add(java.lang.String name, java.lang.String value)
Add a name=value pair WARNING: This method does NOT change the FORMAT field. Use VcfEntry.addFormat() method
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depth
public int depth()
Depth of coverage- Returns:
- -1 if not found
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get
public java.lang.String get(java.lang.String fieldName)
Get a genotype field
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getGenotype
public int[] getGenotype()
Get genotype numbers as an array E.g. '0/1' -> {0, 1} WARNING: If the genotype is missing, the numeric value is '-1'. E.g.: './.' -> {-1, -1}- Returns:
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getGenotype
public java.lang.String getGenotype(int idx)
Get genotype string by index WARNING: If the genotype is missing, it returns an empty string. E.g.: './.' -> getGenotype(0) = ""- Returns:
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getGenotypeCode
public int getGenotypeCode()
Return as a genotype SNP code: -1: if missing data of more than one ALT 0: if aa (0/0) 1: if Aa (0/1 or 1/0) 2: if AA (1/1) WARNING: In multi-allelic case, any non-ref is treated as ALT- Returns:
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getGenotypeCodeIgnoreMissing
public int getGenotypeCodeIgnoreMissing()
Return as a genotype SNP code: 0: if aa (0/0) or any missing value 1: if Aa (0/1 or 1/0) 2: if AA (1/1)- Returns:
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getGenotypeStr
public java.lang.String getGenotypeStr()
Return genotypes as string (e.g. "A/C")- Returns:
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getVcfEntry
public VcfEntry getVcfEntry()
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isHeterozygous
public boolean isHeterozygous()
Is the most likely genotype heterozygous?- Returns:
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isHomozygous
public boolean isHomozygous()
Is this genotype homozygous? (either REF or ALT)
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isHomozygousAlt
public boolean isHomozygousAlt()
Is this genotype homozygous ALT?
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isMissing
public boolean isMissing()
Is genotpye missing (e.g. "GT=./.")- Returns:
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isPhased
public boolean isPhased()
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isRef
public boolean isRef()
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)
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isVariant
public boolean isVariant()
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)
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plodity
public int plodity()
Genotype plodity (i.e. how many copies of the chromosome does it have)
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set
public void set(java.lang.String gtFieldName, java.lang.String gtValue)
Set a genotype field value
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setGenotype
public void setGenotype(java.lang.String gtValue)
Set genotype value
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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