Package org.snpeff.binseq.coder
Class DnaQualityCoder
- java.lang.Object
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- org.snpeff.binseq.coder.Coder
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- org.snpeff.binseq.coder.DnaCoder
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- org.snpeff.binseq.coder.DnaQualityCoder
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- All Implemented Interfaces:
java.io.Serializable
public class DnaQualityCoder extends DnaCoder
Class used to encode & decode sequences into binary and vice-versa - Every base is encoded in 8 bits: - Six bits for the base quality [0 , .. , 63] - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3}- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static int
MAX_QUALITY
static int
MIN_QUALITY
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Fields inherited from class org.snpeff.binseq.coder.DnaCoder
BASES_PER_LONGWORD, BITS_PER_BASE, COUNT_DIFFS, debug, LAST_BASE_IN_LONGWORD, MASK_ALL_WORD, MASK_BASE, MASK_FIRST_BASE, MASK_HIGH, MASK_LOW, TO_BASE
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Fields inherited from class org.snpeff.binseq.coder.Coder
BITS_PER_LONGWORD, BYTES_PER_LONGWORD
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
basesPerWord()
How many bases can we pack in a wordint
baseToBits(char c, int quality)
static DnaQualityCoder
get()
int
qualityToBits(int quality)
WARNING: This implementation transforms the quality to a range [0, ..., 63] (in order to use 6 bits)int
replaceQuality(byte code, int newQuality)
Replace quality value in a given codechar
toBase(int code)
Decode a base using 2 bitsint
toQuality(int code)
Decode a quality-
Methods inherited from class org.snpeff.binseq.coder.DnaCoder
baseToBits, baseToBits, bitsPerBase, copyBases, copyBases, decodeWord, encodeWord, lastBaseinWord, length2words, mask, replaceBase, reverseBases, score, toBase
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Field Detail
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MAX_QUALITY
public static final int MAX_QUALITY
- See Also:
- Constant Field Values
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MIN_QUALITY
public static final int MIN_QUALITY
- See Also:
- Constant Field Values
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Method Detail
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get
public static DnaQualityCoder get()
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basesPerWord
public int basesPerWord()
Description copied from class:Coder
How many bases can we pack in a word- Overrides:
basesPerWord
in classDnaCoder
- Returns:
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baseToBits
public int baseToBits(char c, int quality)
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qualityToBits
public int qualityToBits(int quality)
WARNING: This implementation transforms the quality to a range [0, ..., 63] (in order to use 6 bits)- Overrides:
qualityToBits
in classCoder
- Returns:
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replaceQuality
public int replaceQuality(byte code, int newQuality)
Replace quality value in a given code- Parameters:
code
-newQuality
-- Returns:
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toBase
public char toBase(int code)
Decode a base using 2 bits
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