public abstract class DownsamplingIterator extends java.lang.Object implements CloseableIterator<SAMRecord>
Constructor and Description |
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DownsamplingIterator(double targetProportion)
Constructs a downsampling iterator that aims to retain the targetProportion of reads.
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Modifier and Type | Method and Description |
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void |
close()
Does nothing.
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long |
getAcceptedCount()
Returns the number of records returned since creation of the last call to resetStatistics.
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double |
getAcceptedFraction()
Gets the fraction of records accepted since creation or the last call to resetStatistics().
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long |
getDiscardedCount()
Returns the number of records discarded since creation of the last call to resetStatistics.
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double |
getDiscardedFraction()
Gets the fraction of records discarded since creation or the last call to resetStatistics().
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long |
getSeenCount()
Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.
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double |
getTargetProportion()
Gets the target proportion of records that should be retained during downsampling.
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boolean |
isHigherAccuracy()
Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to
increase accuracy beyond random sampling (i.e.
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protected void |
recordAcceptedRecord()
Method for subclasses to record a specific record as being accepted.
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protected void |
recordAcceptedRecords(long n)
Record one or more records as having been discarded.
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protected void |
recordDiscardedRecord()
Method for subclasses to record a record as being discarded.
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protected void |
recordDiscardRecords(long n)
Record one or more records as having been discarded.
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void |
remove()
Not supported.
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void |
resetStatistics()
Resets the statistics for records seen/accepted/discarded.
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
stream, toList
public DownsamplingIterator(double targetProportion)
public void close()
close
in interface CloseableIterator<SAMRecord>
close
in interface java.io.Closeable
close
in interface java.lang.AutoCloseable
public long getSeenCount()
public long getAcceptedCount()
public long getDiscardedCount()
public double getDiscardedFraction()
public double getAcceptedFraction()
public void resetStatistics()
public double getTargetProportion()
protected final void recordDiscardedRecord()
protected final void recordAcceptedRecord()
protected final void recordDiscardRecords(long n)
protected final void recordAcceptedRecords(long n)
public boolean isHigherAccuracy()
public void remove()
remove
in interface java.util.Iterator<SAMRecord>