Package org.snpsift.annotate.mem.database

Class VariantDataFrame

java.lang.Object
org.snpsift.annotate.mem.database.VariantDataFrame
All Implemented Interfaces:
Serializable
public class VariantDataFrame extends Object implements 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:

  • Constructor Details

  • Method Details

    • load

      public static VariantDataFrame load(String fileName, boolean emptyIfNotFound)

    • annotate

      public int annotate(org.snpeff.vcf.VcfEntry vcfEntry, String[] fieldNames)
      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

      public DataFrame getDataFrameByVariantType(org.snpeff.interval.Variant variant)
      Select the appropirate data set for a variant

    • getDataFrameByCategory

      public DataFrame getDataFrameByCategory(VariantCategory category)

    • setPrefix

      public void setPrefix(String prefix)

    • sizeBytes

      public long sizeBytes()

    • toString

      public String toString()
      Overrides:
      toString in class Object