public class GenotypeCorrection
extends java.lang.Object
Class GenotypeCorrection
removes any inconsistencies between
haplotype pairs and genotypes that determine genotype likelihoods.
Modifier and Type | Method and Description |
---|---|
static void |
run(java.util.List<HapPair> hapPairs,
GL gl,
long seed)
Removes any inconsistencies between the specified list of
haplotype pairs and the genotypes determined by the
allele1()
and allele2() methods of the specified genotype likelihoods. |
static void |
run(java.util.List<HapPair> hapPairs,
GL gl,
long seed,
java.io.File outFile,
boolean append)
Removes any inconsistencies between the specified list of
haplotype pairs and the genotypes determined by the
allele1()
and allele2() methods of the specified genotype likelihoods. |
public static void run(java.util.List<HapPair> hapPairs, GL gl, long seed)
allele1()
and allele2()
methods of the specified genotype likelihoods.
Inconsistencies are resolved by changing the minimum number
of alleles in the haplotype pairs.hapPairs
- a list of haplotype pairsgl
- genotype likelihoodsseed
- a seed for generating random numbersjava.lang.IllegalArgumentException
- if
hapPairs.get(j).markers().equals(gl.markers()) == false
for any j
satisfying (0 <= j && j < hapPairs.size())
java.lang.IllegalArgumentException
- if
hapPairs.get(j).samples().equals(gl.samples()) == false
for any j
satisfying (0 <= j && j < hapPairs.size())
java.lang.NullPointerException
- if hapPairs == null || gl == null
,
or if (hapPair.get(j) == null)
for any j
satisfying
(0 <= j && j < hapPairs.size())
public static void run(java.util.List<HapPair> hapPairs, GL gl, long seed, java.io.File outFile, boolean append)
allele1()
and allele2()
methods of the specified genotype likelihoods.
Inconsistencies are resolved by changing the minimum number
of alleles in the haplotype pairs.hapPairs
- a list of haplotype pairsgl
- genotype likelihoodsseed
- a seed for generating random numbersoutFile
- an output file to which a record of the
genotype changes will be writtenappend
- true
if the genotype changes should be
written to the end of the specified output filejava.lang.IllegalArgumentException
- if
hapPairs.get(j).markers().equals(gl.markers()) == false
for any j
satisfying (0 <= j && j < hapPairs.size())
java.lang.IllegalArgumentException
- if
hapPairs.get(j).samples().equals(gl.samples()) == false
for any j
satisfying (0 <= j && j < hapPairs.size())
java.lang.NullPointerException
- if
(hapPairs == null || gl == null || outFile == null)
,
or if hapPair.get(j) == null
for any j
satisfying
(0 <= j && j < hapPairs.size())