Package imp

Class ImputedVcfWriter

java.lang.Object

imp.ImputedVcfWriter

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 Summary

Constructors

Constructor	Description
ImputedVcfWriter(ImpData impData, int refStart, int refEnd, int targCluster)	Constructs a new ImputedVcfWriter instance from the specified data.

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImputedVcfWriter

public ImputedVcfWriter(ImpData impData,
                        int refStart,
                        int refEnd,
                        int targCluster)

Constructs a new ImputedVcfWriter instance from the specified data.

Parameters:

impData - the input data for genotype imputation

targCluster - the index of the target marker cluster in the interval of reference markers that will be printed

refStart - an lower bound (inclusive) on the reference markers that will be printed

refEnd - an upper bound (exclusive) on the reference markers that will be printed

Throws:

java.lang.IndexOutOfBoundsException - if (refStart < 0 || refEnd > impData.refGT().nMarkers())

java.lang.IndexOutOfBoundsException - if targCluster < 0 || targCluster >= impData.nClusters()

java.lang.NullPointerException - if impData == null

Method Detail

appendRecords

public void appendRecords(java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs,
                          java.io.PrintWriter out)

Writes the VCF records to the specified PrintWriter.

Parameters:

stateProbs - the imputed state probabilities at genotyped markers in the target samples

out - the PrintWriter to which VCF records will be written

Throws:

java.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)