Package htsjdk.samtools
Class ReservedTagConstants
- java.lang.Object
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- htsjdk.samtools.ReservedTagConstants
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public class ReservedTagConstants extends Object
Constants for tags used in our SAM/BAM files
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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 correctionstatic String
OQ
The original pred quality scores before modifications such as 454 cafie and homopolymer correctionstatic String
PROGRAM_GROUP_ID
static String
READ_GROUP_ID
static String
XF
The Four54 edit string of 454 cafie and homopolymer correctionsstatic 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 correctionstatic 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.
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Constructor Summary
Constructors Constructor Description ReservedTagConstants()
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Field Detail
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READ_GROUP_ID
public static final String READ_GROUP_ID
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PROGRAM_GROUP_ID
public static final String PROGRAM_GROUP_ID
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XN
public static final String XN
Present and set to 1 if a read is a noise read.- See Also:
- Constant Field Values
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NM
public static final String NM
Number of nucleotide differences (Specified in the SAM spec doc)
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XQ
public static final String XQ
The sum of the mismatched qualities.- See Also:
- Constant Field Values
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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
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XS
public static final String XS
The original sequence before 454 cafie and homopolymer correction- See Also:
- Constant Field Values
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XF
public static final String XF
The Four54 edit string of 454 cafie and homopolymer correctionseditString ::= {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
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OQ
public static final String OQ
The original pred quality scores before modifications such as 454 cafie and homopolymer correction
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OC
public static final String OC
The original cigar before indel cleaning, or 454 cafie and homopolymer correction- See Also:
- Constant Field Values
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