Package sample
Class InitTargHapPairs
- java.lang.Object
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- sample.InitTargHapPairs
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public final class InitTargHapPairs extends java.lang.Object
Class
InitTargHapPairs
has a static method for returning initial target haplotype pairs.Instances of class
InitTargHapPairs
are immutable.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.util.List<LongArray>
run(GT targ, GT ref, double minFreq, long seed)
Returns initial target haplotype pairs.
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Method Detail
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run
public static java.util.List<LongArray> run(GT targ, GT ref, double minFreq, long seed)
Returns initial target haplotype pairs. Missing alleles are sampled according from the empirical allele frequency distribution, and input genotypes with unknown phase will have their alleles randomly ordered in the returned haplotype pairs.- Parameters:
targ
- the target genotype dataref
- the reference haplotype pairsminFreq
- a minimum allele frequency to be enforcedseed
- the seed for random number generation- Returns:
- initial target haplotype pairs
- Throws:
java.lang.IllegalArgumentException
- ifminFreq <= 0.0 || minFreq >= 0.5 || Double.isNaN(minFreq) == true
java.lang.NullPointerException
- ifgl == null || refHapPairs == null
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