case class GenomeBins(binSize: Long, seqLengths: Map[String, Long]) extends Serializable with Product
Partition a genome into a set of bins.
Note that this class will not tolerate invalid input, so filter in advance if you use it.
- binSize
The size of each bin in nucleotides
- seqLengths
A map containing the length of each contig
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new
GenomeBins(binSize: Long, seqLengths: Map[String, Long])
- binSize
The size of each bin in nucleotides
- seqLengths
A map containing the length of each contig
Value Members
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- val binSize: Long
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def
get(region: ReferenceRegion, useStart: Boolean = true): Int
Get the bin number corresponding to a query ReferenceRegion.
Get the bin number corresponding to a query ReferenceRegion.
- region
the query ReferenceRegion
- useStart
whether to use the start or end point of region to pick the bin
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def
getClass(): Class[_]
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def
getEndBin(region: ReferenceRegion): Int
Get the bin number corresponding to the end of the query ReferenceRegion.
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def
getStartBin(region: ReferenceRegion): Int
Get the bin number corresponding to the start of the query ReferenceRegion.
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def
invert(bin: Int): ReferenceRegion
Given a bin number, return its corresponding ReferenceRegion.
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def
numBins: Int
The total number of bins induced by this partition.
- val seqLengths: Map[String, Long]
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(Since version ) see corresponding Javadoc for more information.