public class QualityScoreAndErrorGenerator
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
static char[] |
encodedSangerQualityScores |
| Constructor and Description |
|---|
QualityScoreAndErrorGenerator(int readLength,
boolean useRealQualityScores,
boolean simulateErrorInRead,
java.lang.String fastq1ForQualityScoresPath,
java.lang.String fastq2ForQualityScoresPath)
Initialise a new QualityScoreAndErrorGenerator object.
|
| Modifier and Type | Method and Description |
|---|---|
long |
getNumACGTBasesCalled()
Get the number of ACGT bases.
|
long |
getNumBaseCallErrors()
Get the number of base call errors that have been simulated.
|
java.util.ArrayList<char[]> |
getQualityScoresAndGenotypesRead(boolean isLeft,
java.util.ArrayList<Nucleobase> nucleobases)
Get the encoded phred quality scores and the genotypes read.
|
void |
resetNumBaseCallErrors()
Reset the number of simulated base call errors to 0.
|
public QualityScoreAndErrorGenerator(int readLength,
boolean useRealQualityScores,
boolean simulateErrorInRead,
java.lang.String fastq1ForQualityScoresPath,
java.lang.String fastq2ForQualityScoresPath)
readLength - - the length of each read.useRealQualityScores - - true if using quality scores from an existing fastq file, else false.simulateErrorInRead - - true if simulating error in reads, else false.fastq1ForQualityScoresPath - - the 1st fastq file whose quality scores are used.fastq2ForQualityScoresPath - - the 2nd fastq file whose quality scores are used.public java.util.ArrayList<char[]> getQualityScoresAndGenotypesRead(boolean isLeft,
java.util.ArrayList<Nucleobase> nucleobases)
isLeft - - true if the read is a left read, else false.nucleobases - - human reference sequence nucleobases which the read is a read of.public long getNumBaseCallErrors()
public void resetNumBaseCallErrors()
public long getNumACGTBasesCalled()