public class DownsamplingIteratorFactory
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
DownsamplingIteratorFactory.Strategy
Describes the available downsampling strategies.
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Modifier and Type | Field and Description |
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static java.lang.String |
CHAINED_DESCRIPTION |
static java.lang.String |
CONSTANT_MEMORY_DESCRPTION |
static java.lang.String |
HIGH_ACCURACY_DESCRIPTION |
Constructor and Description |
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DownsamplingIteratorFactory() |
Modifier and Type | Method and Description |
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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.
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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.
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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.
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public static final java.lang.String HIGH_ACCURACY_DESCRIPTION
public static final java.lang.String CONSTANT_MEMORY_DESCRPTION
public static final java.lang.String CHAINED_DESCRIPTION
public static DownsamplingIterator make(java.util.Iterator<SAMRecord> iterator, DownsamplingIteratorFactory.Strategy strategy, double proportion, double accuracy, int seed)
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.public static DownsamplingIterator make(java.io.File samFile, DownsamplingIteratorFactory.Strategy strategy, double proportion, double accuracy, int seed)
make(Iterator, Strategy, double, double, int)
for detailed parameter information.public static DownsamplingIterator make(SamReader reader, DownsamplingIteratorFactory.Strategy strategy, double proportion, double accuracy, int seed)
make(Iterator, Strategy, double, double, int)
for detailed parameter information.