Package org.snpeff.binseq.coder
Class DnaQualityCoder
java.lang.Object
org.snpeff.binseq.coder.Coder
org.snpeff.binseq.coder.DnaCoder
org.snpeff.binseq.coder.DnaQualityCoder
- All Implemented Interfaces:
Serializable
Class used to encode invalid input: '&' 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} invalid input: '<'=> {0, 1, 2, 3}
- Author:
- pcingola
- See Also:
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Field Summary
FieldsFields 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
Fields inherited from class org.snpeff.binseq.coder.Coder
BITS_PER_LONGWORD, BYTES_PER_LONGWORD
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Method Summary
Modifier and TypeMethodDescriptionint
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 qualityMethods 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 Details
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MAX_QUALITY
public static final int MAX_QUALITY- See Also:
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MIN_QUALITY
public static final int MIN_QUALITY- See Also:
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Method Details
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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) -
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 -
toQuality
public int toQuality(int code) Description copied from class:Coder
Decode a quality
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