Package htsjdk.samtools

Class ReservedTagConstants

  • public class ReservedTagConstants
extends Object
    Constants for tags used in our SAM/BAM files

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String NM
      Number of nucleotide differences (Specified in the SAM spec doc)
      static String OC
      The original cigar before indel cleaning, or 454 cafie and homopolymer correction
      static String OQ
      The original pred quality scores before modifications such as 454 cafie and homopolymer correction
      static String PROGRAM_GROUP_ID  
      static String READ_GROUP_ID  
      static String XF
      The Four54 edit string of 454 cafie and homopolymer corrections
      static String XN
      Present and set to 1 if a read is a noise read.
      static String XQ
      The sum of the mismatched qualities.
      static String XS
      The original sequence before 454 cafie and homopolymer correction
      static String XT
      The name of an attribute which stores the 1-based index of the start of sequence within a read (in original orientation) that should be clipped or trimmed before alignment and downstream use.

    • Field Detail

      • READ_GROUP_ID

        public static final String READ_GROUP_ID

      • PROGRAM_GROUP_ID

        public static final String PROGRAM_GROUP_ID

      • NM

        public static final String NM
        Number of nucleotide differences (Specified in the SAM spec doc)

      • XT

        public static final String XT
        The name of an attribute which stores the 1-based index of the start of sequence within a read (in original orientation) that should be clipped or trimmed before alignment and downstream use. The region to be clipped extends from this position to the end of the read.
        See Also:
        Constant Field Values

      • XF

        public static final String XF
        The Four54 edit string of 454 cafie and homopolymer corrections 
           editString ::= {base operator position [- position]}* ;  // Cafie needs 2 positions
   base ::= A | T | G | C | N ;   // N only for undercall
   operator ::= o | u | c ;       // o = Overcall, u = Undercall, c = Cafie.
   position is 0 based position of the correction (assuming forward strand) .  Cafie positions are to-from.
   For example: XF :Z:Gc4-6Nu11Co15 means a cafie correction moved a G from position 6 to 4,
   an N was inserted for an undercall at position 11, and a C was removed as an overcall at position 15
        See Also:
        Constant Field Values

      • OQ

        public static final String OQ
        The original pred quality scores before modifications such as 454 cafie and homopolymer correction

      • OC

        public static final String OC
        The original cigar before indel cleaning, or 454 cafie and homopolymer correction
        See Also:
        Constant Field Values

    • Constructor Detail

      • ReservedTagConstants

        public ReservedTagConstants()