Package htsjdk.samtools

Class DownsamplingIterator

java.lang.Object
htsjdk.samtools.DownsamplingIterator
All Implemented Interfaces:
CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>
public abstract class DownsamplingIterator extends Object implements CloseableIterator<SAMRecord>
Abstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded. A DownsamplingIterator is an iterator that takes another iterator of SAMRecords and filters out a subset of those records in a random way, while ensuring that all records for a template (i.e. record name) are either retained or discarded. Strictly speaking the proportion parameter applies to templates, though in most instances it is safe to think about it being applied to records.

  • Constructor Summary

    Constructors
    Constructor
    Description
    DownsamplingIterator(double targetProportion)
    Constructs a downsampling iterator that aims to retain the targetProportion of reads.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
    Does nothing.
    long
    getAcceptedCount()
    Returns the number of records returned since creation of the last call to resetStatistics.
    double
    getAcceptedFraction()
    Gets the fraction of records accepted since creation or the last call to resetStatistics().
    long
    getDiscardedCount()
    Returns the number of records discarded since creation of the last call to resetStatistics.
    double
    getDiscardedFraction()
    Gets the fraction of records discarded since creation or the last call to resetStatistics().
    long
    getSeenCount()
    Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.
    double
    getTargetProportion()
    Gets the target proportion of records that should be retained during downsampling.
    boolean
    isHigherAccuracy()
    Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to increase accuracy beyond random sampling (i.e.
    protected final void
    recordAcceptedRecord()
    Method for subclasses to record a specific record as being accepted.
    protected final void
    recordAcceptedRecords(long n)
    Record one or more records as having been discarded.
    protected final void
    recordDiscardedRecord()
    Method for subclasses to record a record as being discarded.
    protected final void
    recordDiscardRecords(long n)
    Record one or more records as having been discarded.
    void
    remove()
    Not supported.
    void
    resetStatistics()
    Resets the statistics for records seen/accepted/discarded.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface htsjdk.samtools.util.CloseableIterator

    stream, toList

    Methods inherited from interface java.util.Iterator

    forEachRemaining, hasNext, next

  • Constructor Details

    • DownsamplingIterator

      public DownsamplingIterator(double targetProportion)
      Constructs a downsampling iterator that aims to retain the targetProportion of reads.

  • Method Details

    • close

      public void close()
      Does nothing.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface CloseableIterator<SAMRecord>

    • getSeenCount

      public long getSeenCount()
      Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.

    • getAcceptedCount

      public long getAcceptedCount()
      Returns the number of records returned since creation of the last call to resetStatistics.

    • getDiscardedCount

      public long getDiscardedCount()
      Returns the number of records discarded since creation of the last call to resetStatistics.

    • getDiscardedFraction

      public double getDiscardedFraction()
      Gets the fraction of records discarded since creation or the last call to resetStatistics().

    • getAcceptedFraction

      public double getAcceptedFraction()
      Gets the fraction of records accepted since creation or the last call to resetStatistics().

    • resetStatistics

      public void resetStatistics()
      Resets the statistics for records seen/accepted/discarded.

    • getTargetProportion

      public double getTargetProportion()
      Gets the target proportion of records that should be retained during downsampling.

    • recordDiscardedRecord

      protected final void recordDiscardedRecord()
      Method for subclasses to record a record as being discarded.

    • recordAcceptedRecord

      protected final void recordAcceptedRecord()
      Method for subclasses to record a specific record as being accepted. Null may be passed if a record was discarded but access to the object is no longer available.

    • recordDiscardRecords

      protected final void recordDiscardRecords(long n)
      Record one or more records as having been discarded.

    • recordAcceptedRecords

      protected final void recordAcceptedRecords(long n)
      Record one or more records as having been discarded.

    • isHigherAccuracy

      public boolean isHigherAccuracy()
      Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to increase accuracy beyond random sampling (i.e. to reduce the delta between the requested proportion of reads and the actually emitted proportion of reads).

    • remove

      public void remove()
      Not supported.
      Specified by:
      remove in interface Iterator<SAMRecord>