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