Package htsjdk.variant.vcf

Class VCFPercentEncodedTextTransformer

java.lang.Object
htsjdk.variant.vcf.VCFPercentEncodedTextTransformer
All Implemented Interfaces:
VCFTextTransformer
public class VCFPercentEncodedTextTransformer extends Object implements VCFTextTransformer
Text transformer for attribute values embedded in VCF. VCF version 4.3 supports percent-encoding of characters that have special meaning in VCF.

  • Constructor Details

    • VCFPercentEncodedTextTransformer

      public VCFPercentEncodedTextTransformer()

  • Method Details

    • decodeText

      public String decodeText(String rawPart)
      Transform a single string, replacing % encoded values with their corresponding text.
      Specified by:
      decodeText in interface VCFTextTransformer
      Parameters:
      rawPart - the raw string to be decoded
      Returns:
      the decoded string
      Throws:
      TribbleException - if the the encoding is uninterpretable

    • decodeText

      public List<String> decodeText(List<String> rawParts)
      Transform a list of strings, replacing % encoded values with their corresponding text in each string.
      Specified by:
      decodeText in interface VCFTextTransformer
      Parameters:
      rawParts - a list of raw strings
      Returns:
      a list of decoded strings
      Throws:
      TribbleException - if the the encoding is uninterpretable

    • decodePercentEncodedChars

      protected static String decodePercentEncodedChars(String rawText)
      Transform input strings containing embedded percent=encoded characters. For example, when given the string '%3D%41' will return the string '=A'.
      Parameters:
      rawText - a string containing zero or more embedded encodings
      Returns:
      a string with all encoded characters replaced with the corresponding character
      Throws:
      TribbleException - if the the encoding is uninterpretable