Package org.snpeff.binseq.coder
Class Coder
java.lang.Object
org.snpeff.binseq.coder.Coder
- All Implemented Interfaces:
Serializable
- Direct Known Subclasses:
DnaCoder
Class used to encode & decode sequences into binary and vice-versa
They are usually stored in 'long' words
- Author:
- pcingola
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionabstract int
How many bases can we pack in a wordabstract int
baseToBits
(char c) Encode a base using a binary representationabstract int
How many bits do we need for each baseabstract int
decodeWord
(long word, int pos) Decode bits from a given position in a wordabstract int
Index of the last base coded in a wordabstract long
mask
(int baseIndexInWord) Bitmask for a base in a wordint
qualityToBits
(int q) Encode a quality using a binary representationabstract char
toBase
(int code) Decode a base using a binary representationabstract char
toBase
(long word, int pos) Decode a base from a given position in a wordint
toQuality
(int code) Decode a quality
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Field Details
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BITS_PER_LONGWORD
public static final int BITS_PER_LONGWORD- See Also:
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BYTES_PER_LONGWORD
public static final int BYTES_PER_LONGWORD- See Also:
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Constructor Details
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Coder
public Coder()
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Method Details
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basesPerWord
public abstract int basesPerWord()How many bases can we pack in a word- Returns:
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baseToBits
public abstract int baseToBits(char c) Encode a base using a binary representation- Parameters:
c
-- Returns:
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bitsPerBase
public abstract int bitsPerBase()How many bits do we need for each base- Returns:
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decodeWord
public abstract int decodeWord(long word, int pos) Decode bits from a given position in a word- Parameters:
word
-pos
-- Returns:
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lastBaseinWord
public abstract int lastBaseinWord()Index of the last base coded in a word- Returns:
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mask
public abstract long mask(int baseIndexInWord) Bitmask for a base in a word- Returns:
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qualityToBits
public int qualityToBits(int q) Encode a quality using a binary representation- Parameters:
c
-- Returns:
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toBase
public abstract char toBase(int code) Decode a base using a binary representation- Parameters:
c
-- Returns:
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toBase
public abstract char toBase(long word, int pos) Decode a base from a given position in a word- Parameters:
word
-pos
-- Returns:
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toQuality
public int toQuality(int code) Decode a quality- Parameters:
c
-- Returns:
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