Package htsjdk.samtools

Class ReservedTagConstants

java.lang.Object

htsjdk.samtools.ReservedTagConstants

public class ReservedTagConstants
extends Object

Constants for tags used in our SAM/BAM files

Field Summary

Fields

Modifier and Type	Field	Description
static final String	NM	Number of nucleotide differences (Specified in the SAM spec doc)
static final String	OC	The original cigar before indel cleaning, or 454 cafie and homopolymer correction
static final String	OQ	The original pred quality scores before modifications such as 454 cafie and homopolymer correction
static final String	PROGRAM_GROUP_ID
static final String	READ_GROUP_ID
static final String	XF	The Four54 edit string of 454 cafie and homopolymer corrections
static final String	XN	Present and set to 1 if a read is a noise read.
static final String	XQ	The sum of the mismatched qualities.
static final String	XS	The original sequence before 454 cafie and homopolymer correction
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.

Constructor Summary

Constructors

Constructor	Description
ReservedTagConstants()

Method Summary

Methods inherited from class java.lang.Object

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

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

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 Details

ReservedTagConstants

public ReservedTagConstants()