Package | Description |
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htsjdk.samtools.util |
Modifier and Type | Method and Description |
---|---|
static FastqQualityFormat |
QualityEncodingDetector.detect(FastqReader... readers) |
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
CloseableIterator<SAMRecord> iterator,
boolean useOriginalQualities)
Reads through the records in the provided SAM reader and uses their quality scores to determine the quality
format used in the SAM.
|
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
FastqReader... readers)
Reads through the records in the provided fastq reader and uses their quality scores to determine the quality
format used in the fastq.
|
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
SamReader reader) |
static FastqQualityFormat |
QualityEncodingDetector.detect(SamReader reader) |
static FastqQualityFormat |
QualityEncodingDetector.detect(SamReader reader,
FastqQualityFormat expectedQualityFormat)
Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
quality passed in.
|
FastqQualityFormat |
QualityEncodingDetector.generateBestGuess(QualityEncodingDetector.FileContext context,
FastqQualityFormat expectedQuality)
Make the best guess at the quality format.
|
static FastqQualityFormat |
FastqQualityFormat.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static FastqQualityFormat[] |
FastqQualityFormat.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
EnumSet<FastqQualityFormat> |
QualityEncodingDetector.generateCandidateQualities(boolean checkExpected)
Processes collected quality data and applies rules to determine which quality formats are possible.
|
Modifier and Type | Method and Description |
---|---|
static FastqQualityFormat |
QualityEncodingDetector.detect(SamReader reader,
FastqQualityFormat expectedQualityFormat)
Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
quality passed in.
|
FastqQualityFormat |
QualityEncodingDetector.generateBestGuess(QualityEncodingDetector.FileContext context,
FastqQualityFormat expectedQuality)
Make the best guess at the quality format.
|