Package htsjdk.samtools
Class DownsamplingIteratorFactory
java.lang.Object
htsjdk.samtools.DownsamplingIteratorFactory
A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while
meeting various criteria.
-
Nested Class Summary
Modifier and TypeClassDescriptionstatic enum
Describes the available downsampling strategies. -
Field Summary
-
Constructor Summary
-
Method Summary
Modifier and TypeMethodDescriptionstatic 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.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.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.
-
Field Details
-
HIGH_ACCURACY_DESCRIPTION
- See Also:
-
CONSTANT_MEMORY_DESCRPTION
- See Also:
-
CHAINED_DESCRIPTION
- See Also:
-
-
Constructor Details
-
DownsamplingIteratorFactory
public DownsamplingIteratorFactory()
-
-
Method Details
-
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.
-
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. -
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.
-