Class VariantDataFrame
java.lang.Object
org.snpsift.annotate.mem.database.VariantDataFrame
- All Implemented Interfaces:
Serializable
A DataFrame of variant's data that is indexed "variant type AND chromosome possition".
We create an "DataFrame" for each variant type: SNP(A), SNP(C), SNP(G), SNP(T), INS, DEL, MNP, MIXED, OTHER.
Each DataFrame is indexed by chromosome position. DataFrames have columns for each field to annotate.
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
Annotate a VCF entry with the fields in this VariantDataFramevoid
check()
This is used after creating the data to verify there are no issues with the dataFrames and indecesgetDataFrameByCategory
(VariantCategory category) getDataFrameByVariantType
(org.snpeff.interval.Variant variant) Select the appropirate data set for a variantstatic VariantDataFrame
void
long
toString()
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Constructor Details
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VariantDataFrame
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Method Details
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load
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annotate
Annotate a VCF entry with the fields in this VariantDataFrame -
check
public void check()This is used after creating the data to verify there are no issues with the dataFrames and indeces -
getDataFrameByVariantType
Select the appropirate data set for a variant -
getDataFrameByCategory
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setPrefix
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sizeBytes
public long sizeBytes() -
toString
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