Package vcf

Class MarkerParser

java.lang.Object
vcf.MarkerParser
public final class MarkerParser extends Object

Class MarkerParser is a parser and filter for a VCF record's ID, REF, ALT, QUAL, FILTER, and INFO subfields.

Instances of class MarkerParser are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    MarkerParser(boolean storeId, boolean storeQual, boolean storeFilter, boolean storeInfo)
    Constructs a new MarkerParser instance from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    storeFilter()
    Returns true if the VCF FILTER field will be stored
    boolean
    storeId()
    Returns true if the VCF ID field will be stored
    boolean
    storeInfo()
    Returns true if the VCF INFO field will be stored
    boolean
    storeQual()
    Returns true if the VCF QUAL field will be stored
    String
    toString()
    Returns a string description of this.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • MarkerParser

      public MarkerParser(boolean storeId, boolean storeQual, boolean storeFilter, boolean storeInfo)
      Constructs a new MarkerParser instance from the specified data.
      Parameters:
      storeId - true if a non-missing VCF ID field will be stored
      storeQual - true if non-missing VCF QUAL field will be stored
      storeFilter - true if a non-missing VCF FILTER field will be stored
      storeInfo - true if a non-missing VCF INFO field will be stored

  • Method Details

    • toString

      public String toString()
      Returns a string description of this. The exact details of the description of are unspecified and subject to change.
      Overrides:
      toString in class Object
      Returns:
      a string description of this

    • storeId

      public boolean storeId()
      Returns true if the VCF ID field will be stored
      Returns:
      true if the VCF ID field will be stored

    • storeQual

      public boolean storeQual()
      Returns true if the VCF QUAL field will be stored
      Returns:
      true if the VCF QUAL field will be stored

    • storeFilter

      public boolean storeFilter()
      Returns true if the VCF FILTER field will be stored
      Returns:
      true if the VCF FILTER field will be stored

    • storeInfo

      public boolean storeInfo()
      Returns true if the VCF INFO field will be stored
      Returns:
      true if the VCF INFO field will be stored