Class TextCigarCodec

java.lang.Object
htsjdk.samtools.TextCigarCodec

public class TextCigarCodec extends Object
Convert between String and Cigar class representations of CIGAR.
  • Constructor Details

    • TextCigarCodec

      public TextCigarCodec()
  • Method Details

    • encode

      public static String encode(Cigar cigar)
      Convert from Cigar class representation to String.
      Parameters:
      cigar - in Cigar class format
      Returns:
      CIGAR in String form ala SAM text file. "*" means empty CIGAR.
    • decode

      public static Cigar decode(String textCigar)
      Convert from String CIGAR representation to Cigar class representation. Does not do validation beyond the most basic CIGAR string well-formedness, i.e. each operator is valid, and preceded by a decimal length.
      Parameters:
      textCigar - CIGAR in String form ala SAM text file. "*" means empty CIGAR.
      Returns:
      cigar in Cigar class format
      Throws:
      RuntimeException - if textCigar is invalid at the most basic level.