org.disq_bio.disq

Class HtsjdkVariantsRdd

java.lang.Object

org.disq_bio.disq.HtsjdkVariantsRdd

public class HtsjdkVariantsRdd
extends Object

A HtsjdkVariantsRdd is the distributed equivalent of a htsjdk VCFFileReader. It represents a VCF file stored in a distributed filesystem, and encapsulates a Spark RDD containing the variant records in it.

Use a HtsjdkVariantsRddStorage to read and write HtsjdkVariantsRdds.

See Also:

HtsjdkVariantsRddStorage

Constructor Summary

Constructors

Constructor and Description
HtsjdkVariantsRdd(htsjdk.variant.vcf.VCFHeader header, org.apache.spark.api.java.JavaRDD<htsjdk.variant.variantcontext.VariantContext> variants)

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.vcf.VCFHeader	getHeader()
org.apache.spark.api.java.JavaRDD<htsjdk.variant.variantcontext.VariantContext>	getVariants()

Methods inherited from class java.lang.Object

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

Constructor Detail

HtsjdkVariantsRdd

public HtsjdkVariantsRdd(htsjdk.variant.vcf.VCFHeader header,
                         org.apache.spark.api.java.JavaRDD<htsjdk.variant.variantcontext.VariantContext> variants)

Method Detail

getHeader

public htsjdk.variant.vcf.VCFHeader getHeader()

Returns:

the header for the variants in this RDD. In the case that different variants have different headers, it is undefined which header this method returns.

getVariants

public org.apache.spark.api.java.JavaRDD<htsjdk.variant.variantcontext.VariantContext> getVariants()

Returns:

a RDD of VariantContext with headers.