Class DataFrameSnp

java.lang.Object
org.snpsift.annotate.mem.dataFrame.DataFrame
org.snpsift.annotate.mem.dataFrame.DataFrameSnp
All Implemented Interfaces:
Serializable

public class DataFrameSnp extends DataFrame
The DataFrameSnp class extends the DataFrame class and represents a specific type of data frame that deals with single nucleotide polymorphisms (SNPs). Each instance of DataFrameSnp is associated with a specific alternative allele ('A', 'C', 'G', or 'T') based on the provided variant category. This class provides methods to retrieve the alternative allele and to check if a given entry matches specific position and allele values. Limitations: - The class assumes that the variant category provided during instantiation is one of the SNP categories (SNP_A, SNP_C, SNP_G, SNP_T). If an invalid category is provided, a RuntimeException is thrown. - The eq method assumes that the alternative allele (alt) is always in uppercase. If the provided alt parameter in the eq method is not in uppercase, a RuntimeException is thrown.
See Also:
  • Constructor Details

  • Method Details

    • getAlt

      public String getAlt()
    • eq

      protected boolean eq(int idx, int pos, String ref, String alt)
      Does the entry at possition 'idx' match the given (pos, ref, alt) values?
      Overrides:
      eq in class DataFrame