public class ImputedVcfWriter
extends java.lang.Object
Class ImputedVcfWriter
writes observed and imputed genotypes
to a VCF output file.
Instances of class ImputedVcfWriter
are not thread-safe.
Constructor | Description |
---|---|
ImputedVcfWriter(ImpData impData,
int targCluster,
int refStart,
int refEnd) |
Constructs a new
ImputedVcfWriter instance from
the specified data. |
Modifier and Type | Method | Description |
---|---|---|
void |
appendRecords(java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs,
java.io.PrintWriter out) |
Writes the VCF records to the specified
PrintWriter . |
public ImputedVcfWriter(ImpData impData, int targCluster, int refStart, int refEnd)
ImputedVcfWriter
instance from
the specified data.impData
- the input data for genotype imputationtargCluster
- the index of the target marker cluster in the
interval of reference markers that will be printedrefStart
- an lower bound (inclusive) on the reference markers
that will be printedrefEnd
- an upper bound (exclusive) on the reference markers
that will be printedjava.lang.IndexOutOfBoundsException
- if
(refStart < 0 || refEnd > impData.refGT().nMarkers())
java.lang.IndexOutOfBoundsException
- if
targCluster < 0 || targCluster >= impData.nClusters()
java.lang.NullPointerException
- if impData == null
public void appendRecords(java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs, java.io.PrintWriter out)
PrintWriter
.stateProbs
- the imputed state probabilities at genotyped
markers in the target samplesout
- the PrintWriter
to which VCF records will be writtenjava.lang.NullPointerException
- if stateProbs == null || out == null
java.lang.NullPointerException
- if there exists a j
satisfying
(0 <= j && j < stateProbs.size()) && (stateProbs.get(j) == null)