Package htsjdk.samtools
Class DownsamplingIteratorFactory
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- htsjdk.samtools.DownsamplingIteratorFactory
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public class DownsamplingIteratorFactory extends Object
A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static classDownsamplingIteratorFactory.StrategyDescribes the available downsampling strategies.
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Field Summary
Fields Modifier and Type Field Description static StringCHAINED_DESCRIPTIONstatic StringCONSTANT_MEMORY_DESCRPTIONstatic StringHIGH_ACCURACY_DESCRIPTION
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Constructor Summary
Constructors Constructor Description DownsamplingIteratorFactory()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static DownsamplingIteratormake(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.static DownsamplingIteratormake(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 DownsamplingIteratormake(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.
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Field Detail
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HIGH_ACCURACY_DESCRIPTION
public static final String HIGH_ACCURACY_DESCRIPTION
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- Constant Field Values
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CONSTANT_MEMORY_DESCRPTION
public static final String CONSTANT_MEMORY_DESCRPTION
- See Also:
- Constant Field Values
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CHAINED_DESCRIPTION
public static final String CHAINED_DESCRIPTION
- See Also:
- Constant Field Values
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Method Detail
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make
public static DownsamplingIterator make(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 SAMRecordsstrategy- The downsampling strategy to useproportion- The proportion of records the downsampling strategy should attempt to emitaccuracy- 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.
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make
public static DownsamplingIterator make(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. Seemake(Iterator, Strategy, double, double, int)for detailed parameter information.
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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. Seemake(Iterator, Strategy, double, double, int)for detailed parameter information.
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