Class ReservedTagConstants

Field Details

• READ_GROUP_ID

  public static final String READ_GROUP_ID

• PROGRAM_GROUP_ID

  public static final String PROGRAM_GROUP_ID

• XN

  public static final String XN

  Present and set to 1 if a read is a noise read.

  See Also:

  • Constant Field Values

• NM

  public static final String NM

  Number of nucleotide differences (Specified in the SAM spec doc)

• XQ

  public static final String XQ

  The sum of the mismatched qualities.

  See Also:

  • Constant Field Values

• 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

• XS

  public static final String XS

  The original sequence before 454 cafie and homopolymer correction

  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

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  • 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