DnaQualityCoder (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.binseq.coder.Coder
- - org.snpeff.binseq.coder.DnaCoder
  - - org.snpeff.binseq.coder.DnaQualityCoder

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

Field Summary

Fields
Modifier and Type Field Description

static int MAX_QUALITY

static int MIN_QUALITY
- 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
- Fields inherited from class org.snpeff.binseq.coder.Coder
  BITS_PER_LONGWORD, BYTES_PER_LONGWORD

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 word
`int`	`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 code
`char`	`toBase(int code)`	Decode a base using 2 bits
`int`	`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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MAX_QUALITY
```
public static final int MAX_QUALITY
```
    See Also:
    
    Constant Field Values
  - MIN_QUALITY
```
public static final int MIN_QUALITY
```
    See Also:
    
    Constant Field Values
- Method Detail
  - get
```
public static DnaQualityCoder get()
```
  - basesPerWord
```
public int basesPerWord()
```
    Description copied from class: Coder
    
    How many bases can we pack in a word
    
    Overrides:
    
    basesPerWord in class DnaCoder
    
    Returns:
  - 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 class Coder
    
    Returns:
  - replaceQuality
```
public int replaceQuality(byte code,
                          int newQuality)
```
    Replace quality value in a given code
    
    Parameters:
    
    code -
    
    newQuality -
    
    Returns:
  - toBase
```
public char toBase(int code)
```
    Decode a base using 2 bits
    
    Overrides:
    
    toBase in class DnaCoder
    
    Parameters:
    
    c -
    
    Returns:
  - toQuality
```
public int toQuality(int code)
```
    Description copied from class: Coder
    
    Decode a quality
    
    Overrides:
    
    toQuality in class Coder
    
    Returns: