public class QualityEncodingDetector
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
QualityEncodingDetector.FileContext |
Modifier and Type | Field and Description |
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static long |
DEFAULT_MAX_RECORDS_TO_ITERATE
The maximum number of records over which the detector will iterate before making a determination, by default.
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Constructor and Description |
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QualityEncodingDetector() |
Modifier and Type | Method and Description |
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void |
add(FastqRecord fastqRecord)
Adds the provided record's qualities to the detector.
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long |
add(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
long |
add(long maxRecords,
CloseableIterator<SAMRecord> iterator,
boolean useOriginalQualities)
Adds the provided iterator's records (optionally using the original qualities) to the detector.
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long |
add(long maxRecords,
FastqReader... readers)
Adds the provided reader's records to the detector.
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long |
add(long maxRecords,
SamReader reader)
Adds the provided reader's records to the detector.
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void |
add(SAMRecord samRecord) |
void |
add(SAMRecord samRecord,
boolean useOriginalQualities)
Adds the provided record's qualities to the detector.
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static FastqQualityFormat |
detect(FastqReader... readers) |
static FastqQualityFormat |
detect(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
static FastqQualityFormat |
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.
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static FastqQualityFormat |
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.
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static FastqQualityFormat |
detect(long maxRecords,
SamReader reader) |
static FastqQualityFormat |
detect(SamReader reader) |
static FastqQualityFormat |
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.
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FastqQualityFormat |
generateBestGuess(QualityEncodingDetector.FileContext context,
FastqQualityFormat expectedQuality)
Make the best guess at the quality format.
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java.util.EnumSet<FastqQualityFormat> |
generateCandidateQualities(boolean checkExpected)
Processes collected quality data and applies rules to determine which quality formats are possible.
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boolean |
isDeterminationAmbiguous()
Tests whether or not the detector can make a determination without guessing (i.e., if all but one quality format
can be excluded using established exclusion conventions).
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public static final long DEFAULT_MAX_RECORDS_TO_ITERATE
public long add(long maxRecords, FastqReader... readers)
public long add(long maxRecords, SamReader reader)
public long add(long maxRecords, CloseableIterator<SAMRecord> iterator, boolean useOriginalQualities)
public long add(long maxRecords, CloseableIterator<SAMRecord> iterator)
public void add(FastqRecord fastqRecord)
public void add(SAMRecord samRecord, boolean useOriginalQualities)
public void add(SAMRecord samRecord)
public boolean isDeterminationAmbiguous()
public java.util.EnumSet<FastqQualityFormat> generateCandidateQualities(boolean checkExpected)
public static FastqQualityFormat detect(long maxRecords, FastqReader... readers)
readers
- The fastq readers from which qualities are to be read; at least one must be providedmaxRecords
- The maximum number of records to read from the reader before making a determination (a guess,
so more records is better)public static FastqQualityFormat detect(FastqReader... readers)
public static FastqQualityFormat detect(long maxRecords, CloseableIterator<SAMRecord> iterator, boolean useOriginalQualities)
iterator
- The iterator from which SAM records are to be readmaxRecords
- The maximum number of records to read from the reader before making a determination (a guess,useOriginalQualities
- whether to use the original qualities (if available) rather than the current ones
so more records is better)public static FastqQualityFormat detect(long maxRecords, CloseableIterator<SAMRecord> iterator)
public static FastqQualityFormat detect(long maxRecords, SamReader reader)
public static FastqQualityFormat detect(SamReader reader)
public static FastqQualityFormat detect(SamReader reader, FastqQualityFormat expectedQualityFormat)
SAMException
.public FastqQualityFormat generateBestGuess(QualityEncodingDetector.FileContext context, FastqQualityFormat expectedQuality)