htsjdk.samtools

Class DownsamplingIteratorFactory

java.lang.Object

htsjdk.samtools.DownsamplingIteratorFactory

public class DownsamplingIteratorFactory
extends java.lang.Object

A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DownsamplingIteratorFactory.Strategy Describes the available downsampling strategies.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CHAINED_DESCRIPTION
static java.lang.String	CONSTANT_MEMORY_DESCRPTION
static java.lang.String	HIGH_ACCURACY_DESCRIPTION

Constructor Summary

Constructors

Constructor and Description
DownsamplingIteratorFactory()

Method Summary

Modifier and Type	Method and Description
static DownsamplingIterator	make(java.io.File samFile, DownsamplingIteratorFactory.Strategy strategy, double proportion, double accuracy, int seed) Convenience method that constructs a downsampling iterator for all the reads in a SAM file.
static DownsamplingIterator	make(java.util.Iterator<SAMRecord> iterator, DownsamplingIteratorFactory.Strategy strategy, double proportion, double accuracy, int seed) Creates a new DownsamplingIterator using the supplied Strategy that attempts to read from the provided iterator and return approximately proportion of the records read.
static DownsamplingIterator	make(SamReader reader, DownsamplingIteratorFactory.Strategy strategy, double proportion, double accuracy, int seed) Convenience method that constructs a downsampling iterator for all the reads available from a SamReader.

Methods inherited from class java.lang.Object

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

Field Detail

HIGH_ACCURACY_DESCRIPTION

public static final java.lang.String HIGH_ACCURACY_DESCRIPTION

See Also:

Constant Field Values

CONSTANT_MEMORY_DESCRPTION

public static final java.lang.String CONSTANT_MEMORY_DESCRPTION

See Also:

Constant Field Values

CHAINED_DESCRIPTION

public static final java.lang.String CHAINED_DESCRIPTION

See Also:

Constant Field Values

Constructor Detail

DownsamplingIteratorFactory

public DownsamplingIteratorFactory()

Method Detail

make

public static DownsamplingIterator make(java.util.Iterator<SAMRecord> iterator,
                                        DownsamplingIteratorFactory.Strategy strategy,
                                        double proportion,
                                        double accuracy,
                                        int seed)

Creates a new DownsamplingIterator using the supplied Strategy that attempts to read from the provided iterator and return approximately proportion of the records read.

Parameters:

iterator - The iterator from which to consume SAMRecords

strategy - The downsampling strategy to use

proportion - The proportion of records the downsampling strategy should attempt to emit

accuracy - If supported by the downsampling strategy, the accuracy goal for the downsampler. Higher accuracy will generally require higher memory usage. An accuracy value of 0.0001 tells the strategy to try and ensure the emitted proportion is within proportion +/0 0.0001.

seed - The seed value to use for any random process used in down-sampling.

make

public static DownsamplingIterator make(java.io.File samFile,
                                        DownsamplingIteratorFactory.Strategy strategy,
                                        double proportion,
                                        double accuracy,
                                        int seed)

Convenience method that constructs a downsampling iterator for all the reads in a SAM file. See make(Iterator, Strategy, double, double, int) for detailed parameter information.

make

public static DownsamplingIterator make(SamReader reader,
                                        DownsamplingIteratorFactory.Strategy strategy,
                                        double proportion,
                                        double accuracy,
                                        int seed)

Convenience method that constructs a downsampling iterator for all the reads available from a SamReader. See make(Iterator, Strategy, double, double, int) for detailed parameter information.