org.broadinstitute.hellbender.engine.spark

Class FindAssemblyRegionsSpark

java.lang.Object

org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark

public class FindAssemblyRegionsSpark
extends java.lang.Object

Find assembly regions from reads in a distributed Spark setting. There are two algorithms available, fast, which looks for assembly regions in each read shard in parallel, and strict, which looks for assembly regions in each contig in parallel. Fast mode may produce read shard boundary artifacts for assembly regions compared to the walker version. Strict mode should be identical to the walker version, at the cost of increased runtime compared to the fast version.

Constructor Summary

Constructors

Constructor and Description
FindAssemblyRegionsSpark()

Method Summary

Modifier and Type	Method and Description
static org.apache.spark.api.java.JavaRDD<AssemblyRegionWalkerContext>	getAssemblyRegionsFast(org.apache.spark.api.java.JavaSparkContext ctx, org.apache.spark.api.java.JavaRDD<GATKRead> reads, htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, java.lang.String referenceFileName, FeatureManager features, java.util.List<ShardBoundary> intervalShards, org.apache.spark.broadcast.Broadcast<java.util.function.Supplier<AssemblyRegionEvaluator>> assemblyRegionEvaluatorSupplierBroadcast, AssemblyRegionReadShardArgumentCollection shardingArgs, AssemblyRegionArgumentCollection assemblyRegionArgs, boolean includeReadsWithDeletionsInIsActivePileups, boolean shuffle) Get an RDD of assembly regions for the given reads and intervals using the fast algorithm (looks for assembly regions in each read shard in parallel).
static org.apache.spark.api.java.JavaRDD<AssemblyRegionWalkerContext>	getAssemblyRegionsStrict(org.apache.spark.api.java.JavaSparkContext ctx, org.apache.spark.api.java.JavaRDD<GATKRead> reads, htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, java.lang.String referenceFileName, FeatureManager features, java.util.List<ShardBoundary> intervalShards, org.apache.spark.broadcast.Broadcast<java.util.function.Supplier<AssemblyRegionEvaluator>> assemblyRegionEvaluatorSupplierBroadcast, AssemblyRegionReadShardArgumentCollection shardingArgs, AssemblyRegionArgumentCollection assemblyRegionArgs, boolean includeReadsWithDeletionsInIsActivePileups, boolean shuffle) Get an RDD of assembly regions for the given reads and intervals using the strict algorithm (looks for assembly regions in each contig in parallel).

Methods inherited from class java.lang.Object

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

Constructor Detail

FindAssemblyRegionsSpark

public FindAssemblyRegionsSpark()

Method Detail

getAssemblyRegionsFast

public static org.apache.spark.api.java.JavaRDD<AssemblyRegionWalkerContext> getAssemblyRegionsFast(org.apache.spark.api.java.JavaSparkContext ctx,
                                                                                                    org.apache.spark.api.java.JavaRDD<GATKRead> reads,
                                                                                                    htsjdk.samtools.SAMFileHeader header,
                                                                                                    htsjdk.samtools.SAMSequenceDictionary sequenceDictionary,
                                                                                                    java.lang.String referenceFileName,
                                                                                                    FeatureManager features,
                                                                                                    java.util.List<ShardBoundary> intervalShards,
                                                                                                    org.apache.spark.broadcast.Broadcast<java.util.function.Supplier<AssemblyRegionEvaluator>> assemblyRegionEvaluatorSupplierBroadcast,
                                                                                                    AssemblyRegionReadShardArgumentCollection shardingArgs,
                                                                                                    AssemblyRegionArgumentCollection assemblyRegionArgs,
                                                                                                    boolean includeReadsWithDeletionsInIsActivePileups,
                                                                                                    boolean shuffle)

Get an RDD of assembly regions for the given reads and intervals using the fast algorithm (looks for assembly regions in each read shard in parallel).

Parameters:

ctx - the Spark context

reads - the coordinate-sorted reads

header - the header for the reads

sequenceDictionary - the sequence dictionary for the reads

referenceFileName - the file name for the reference

features - source of arbitrary features (may be null)

intervalShards - the sharded intervals to find assembly regions for

assemblyRegionEvaluatorSupplierBroadcast - evaluator used to determine whether a locus is active

shardingArgs - the arguments for sharding reads

assemblyRegionArgs - the arguments for finding assembly regions

includeReadsWithDeletionsInIsActivePileups - include reads with deletion at loci

shuffle - whether to use a shuffle or not when sharding reads

Returns:

an RDD of assembly regions

getAssemblyRegionsStrict

public static org.apache.spark.api.java.JavaRDD<AssemblyRegionWalkerContext> getAssemblyRegionsStrict(org.apache.spark.api.java.JavaSparkContext ctx,
                                                                                                      org.apache.spark.api.java.JavaRDD<GATKRead> reads,
                                                                                                      htsjdk.samtools.SAMFileHeader header,
                                                                                                      htsjdk.samtools.SAMSequenceDictionary sequenceDictionary,
                                                                                                      java.lang.String referenceFileName,
                                                                                                      FeatureManager features,
                                                                                                      java.util.List<ShardBoundary> intervalShards,
                                                                                                      org.apache.spark.broadcast.Broadcast<java.util.function.Supplier<AssemblyRegionEvaluator>> assemblyRegionEvaluatorSupplierBroadcast,
                                                                                                      AssemblyRegionReadShardArgumentCollection shardingArgs,
                                                                                                      AssemblyRegionArgumentCollection assemblyRegionArgs,
                                                                                                      boolean includeReadsWithDeletionsInIsActivePileups,
                                                                                                      boolean shuffle)

Get an RDD of assembly regions for the given reads and intervals using the strict algorithm (looks for assembly regions in each contig in parallel).

Parameters:

ctx - the Spark context

reads - the coordinate-sorted reads

header - the header for the reads

sequenceDictionary - the sequence dictionary for the reads

referenceFileName - the file name for the reference

features - source of arbitrary features (may be null)

intervalShards - the sharded intervals to find assembly regions for

assemblyRegionEvaluatorSupplierBroadcast - evaluator used to determine whether a locus is active

shardingArgs - the arguments for sharding reads

assemblyRegionArgs - the arguments for finding assembly regions

includeReadsWithDeletionsInIsActivePileups - include reads with deletion at loci

shuffle - whether to use a shuffle or not when sharding reads

Returns:

an RDD of assembly regions