public class ReservedTagConstants extends Object
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.
|
Constructor | Description |
---|---|
ReservedTagConstants() |
public static final String READ_GROUP_ID
public static final String PROGRAM_GROUP_ID
public static final String XN
public static final String NM
public static final String XQ
public static final String XT
public static final String XS
public static final 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 String OQ
public static final String OC