## Class PhredTools

• ```public final class PhredTools
extends Object```

PhredTools contains static methods for working with phred quality data.

Company: AgResearch

Since:
1.1 Note that Phred is a copyright of CodonCode Corporation.
Author:
Mark Schreiber, Matthew Pocock
• ### Constructor Summary

Constructors
Constructor Description
`PhredTools()`
• ### Method Summary

All Methods
Modifier and Type Method Description
`static SymbolList` ```createPhred​(SymbolList dna, SymbolList quality)```
Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
`static Symbol` `dnaSymbolFromPhred​(Symbol phredSym)`
Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
`static FiniteAlphabet` `getPhredAlphabet()`
Retrieves the PHRED alphabet from the AlphabetManager.
`static Symbol` ```getPhredSymbol​(Symbol dna, Symbol integer)```
Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
`static IntegerAlphabet.IntegerSymbol` `integerSymbolFromPhred​(Symbol phredSym)`
Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
`static double` `pFromQuality​(double quality)`
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
`static double` `pFromQuality​(int quality)`
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
`static double` `pFromQuality​(IntegerAlphabet.IntegerSymbol quality)`
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
`static Distribution[]` `phredAlignmentToDistArray​(Alignment a)`
converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
`static Distribution[]` `phredToDistArray​(PhredSequence s)`
Converts a Phred sequence to an array of distributions.
`static double` `qualityFromP​(double probOfError)`
The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.
`static StreamReader` `readPhredQuality​(BufferedReader br)`
Constructs a StreamReader to read in Phred quality data in FASTA format.
`static StreamReader` `readPhredSequence​(BufferedReader br)`
`static void` ```writePhredQuality​(OutputStream qual, OutputStream seq, SequenceDB db)```
Writes Phred quality data in a Fasta type format.
• ### Methods inherited from class java.lang.Object

`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`
• ### Constructor Detail

• #### PhredTools

`public PhredTools()`
• ### Method Detail

• #### getPhredAlphabet

`public static final FiniteAlphabet getPhredAlphabet()`
Retrieves the PHRED alphabet from the AlphabetManager. The Phred alphabet is a cross product of a subset of the IntegerAlphabet from 0...99 and the DNA alphabet. The Phred alphabet is finite. The Phred Alphabet contains 400 BasisSymbols named, for example, (guanine 47). The BasisSymbols can be fragmented into their component AtomicSymbols using the `getSymbols()` method of BasisSymbol.
• #### dnaSymbolFromPhred

```public static final Symbol dnaSymbolFromPhred​(Symbol phredSym)
throws IllegalSymbolException```
Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
Throws:
`IllegalSymbolException` - if the provided symbol is not from the PHRED alphabet.
• #### integerSymbolFromPhred

```public static final IntegerAlphabet.IntegerSymbol integerSymbolFromPhred​(Symbol phredSym)
throws IllegalSymbolException```
Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
Throws:
`IllegalSymbolException` - if the provided symbol is not from the PHRED alphabet.
• #### createPhred

```public static SymbolList createPhred​(SymbolList dna,
SymbolList quality)
throws IllegalArgumentException,
IllegalAlphabetException,
IllegalSymbolException```
Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
Throws:
`IllegalAlphabetException` - if the alphabets are not of the required alphabets
`IllegalArgumentException` - if the two SymbolLists are not of equal length.
`IllegalSymbolException` - if a combination of Symbols cannot be represented by the PHRED alphabet.
• #### getPhredSymbol

```public static final Symbol getPhredSymbol​(Symbol dna,
Symbol integer)
throws IllegalSymbolException```
Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
Throws:
`IllegalSymbolException` - if there is no Symbol in the PHRED alphabet that represents the two arguments.
• #### writePhredQuality

```public static void writePhredQuality​(OutputStream qual,
OutputStream seq,
SequenceDB db)
throws IOException,
BioException```
Writes Phred quality data in a Fasta type format.
Parameters:
`db` - a bunch of PhredSequence objects
`qual` - the OutputStream to write the quality data to.
`seq` - the OutputStream to write the sequence data to.
Throws:
`IOException`
`BioException`
Since:
1.2

`public static StreamReader readPhredQuality​(BufferedReader br)`
Constructs a StreamReader to read in Phred quality data in FASTA format. The data is converted into sequences consisting of Symbols from the IntegerAlphabet.

`public static StreamReader readPhredSequence​(BufferedReader br)`
• #### qualityFromP

`public static double qualityFromP​(double probOfError)`
The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.
Returns:
a `double` value, note that for most Phred scores this will be rounded to the nearest `int`
• #### pFromQuality

`public static double pFromQuality​(double quality)`
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
• #### pFromQuality

`public static double pFromQuality​(int quality)`
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
• #### pFromQuality

`public static double pFromQuality​(IntegerAlphabet.IntegerSymbol quality)`
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
• #### phredToDistArray

`public static Distribution[] phredToDistArray​(PhredSequence s)`
Converts a Phred sequence to an array of distributions. Essentially a fuzzy sequence Assumes that all of the non called bases are equiprobable
• #### phredAlignmentToDistArray

`public static Distribution[] phredAlignmentToDistArray​(Alignment a)`
converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
Throws:
`ClassCastException` - if the sequences in the alignment are not instances of PhredSequence