org.broadinstitute.hellbender.utils.nio

Class NioBam

java.lang.Object

org.broadinstitute.hellbender.utils.nio.NioBam

All Implemented Interfaces:

java.io.Serializable

public class NioBam
extends java.lang.Object
implements java.io.Serializable

NioBam holds a reference to a BAM file on Google Cloud Storage, and can give you an RDD with the reads inside of it. The constructor will open the file to make sure it exists and we have access to it. This is preferable to waiting until we're running on the cloud. Although we don't expect you to move these objects across computers, you can.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.logging.log4j.Logger	logger

Constructor Summary

Constructors

Constructor and Description
NioBam(java.lang.String gcsFilename) Finds the index file, then calls NioBam(bam, index).
NioBam(java.lang.String gcsFilename, java.lang.String indexGcsFilename) Checks the files exists, then stores them.

Method Summary

Modifier and Type	Method and Description
org.apache.spark.api.java.JavaRDD<htsjdk.samtools.SAMRecord>	getReads(org.apache.spark.api.java.JavaSparkContext ctx, int numPartitions) Parses the BAM file into SAMRecords.

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.logging.log4j.Logger logger

Constructor Detail

NioBam

public NioBam(java.lang.String gcsFilename,
              java.lang.String indexGcsFilename)

Checks the files exists, then stores them.

NioBam

public NioBam(java.lang.String gcsFilename)

Finds the index file, then calls NioBam(bam, index).

Method Detail

getReads

public org.apache.spark.api.java.JavaRDD<htsjdk.samtools.SAMRecord> getReads(org.apache.spark.api.java.JavaSparkContext ctx,
                                                                             int numPartitions)

Parses the BAM file into SAMRecords. Will be distributed onto at least 'numPartitions' partitions.