class GroupedSegments extends AnyRef
A collection of counted super-mers grouped into bins (by minimizer). Super-mers are segments of length >= k where every k-mer shares the same minimizer.
Unlike with the Index, every k-mer in the super-mers is guaranteed to be present.
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new
GroupedSegments(segments: Dataset[(BucketId, Array[ZeroNTBitArray], Array[Abundance])], splitter: Broadcast[AnyMinSplitter])(implicit spark: SparkSession)
- segments
The super-mers in binary format, together with their abundances.
- splitter
The read splitter
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- val segments: Dataset[(BucketId, Array[ZeroNTBitArray], Array[Abundance])]
- val splitter: Broadcast[AnyMinSplitter]
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def
superkmerStrings: DataFrame
Convert this dataset to human-readable pairs of (minimizer, super-mer string).
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def
toIndex(filterOrientation: Boolean, numBuckets: Int = 200): Index
Construct a counting index from the input data in these grouped segments
- def toReducibleBuckets(filterOrientation: Boolean): Dataset[ReducibleBucket]
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def
writeSupermerStrings(outputLocation: String): Unit
Write these segments (as pairs of minimizers and strings) to HDFS.
Write these segments (as pairs of minimizers and strings) to HDFS. This action triggers a computation.
- outputLocation
A directory (prefix name) where the super-mers will be stored.