Package org.snpeff.binseq
Class DnaSequenceByte
java.lang.Object
org.snpeff.binseq.DnaSequenceByte
Binary packed DNA sequence.
Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'bytes; - Most significant bits are the first bases in the sequence (makes comparison easier)
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final byte[]
static final char[]
static final int
static final int
static final byte[]
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Constructor Summary
Constructors -
Method Summary
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Field Details
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BASES_PER_BYTE
public static final int BASES_PER_BYTE- See Also:
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BITS_PER_BASE
public static final int BITS_PER_BASE- See Also:
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MASK
public static final byte[] MASK -
BASES
public static final char[] BASES -
BASE2CODE
public static final byte[] BASE2CODE
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Constructor Details
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DnaSequenceByte
public DnaSequenceByte(int length, byte[] codes) -
DnaSequenceByte
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Method Details