org.disq_bio.disq

Class HtsjdkReadsRdd

java.lang.Object

org.disq_bio.disq.HtsjdkReadsRdd

public class HtsjdkReadsRdd
extends Object

A HtsjdkReadsRdd is the distributed equivalent of a htsjdk SamReader. It represents a SAM, BAM, or CRAM file stored in a distributed filesystem, and encapsulates a Spark RDD containing the reads in it.

Use a HtsjdkReadsRddStorage to read and write HtsjdkReadsRdds.

See Also:

HtsjdkReadsRddStorage

Constructor Summary

Constructors

Constructor and Description
HtsjdkReadsRdd(htsjdk.samtools.SAMFileHeader header, org.apache.spark.api.java.JavaRDD<htsjdk.samtools.SAMRecord> reads)

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.SAMFileHeader	getHeader()
org.apache.spark.api.java.JavaRDD<htsjdk.samtools.SAMRecord>	getReads()

Methods inherited from class java.lang.Object

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

Constructor Detail

HtsjdkReadsRdd

public HtsjdkReadsRdd(htsjdk.samtools.SAMFileHeader header,
                      org.apache.spark.api.java.JavaRDD<htsjdk.samtools.SAMRecord> reads)

Method Detail

getHeader

public htsjdk.samtools.SAMFileHeader getHeader()

Returns:

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

getReads

public org.apache.spark.api.java.JavaRDD<htsjdk.samtools.SAMRecord> getReads()

Returns:

a RDD of SAMRecord with headers.