Package org.broadinstitute.hellbender.tools.copynumber

Class CollectAllelicCountsSpark

java.lang.Object
org.broadinstitute.hellbender.cmdline.CommandLineProgram
org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
org.broadinstitute.hellbender.engine.spark.GATKSparkTool
org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
All Implemented Interfaces:
Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider
public class CollectAllelicCountsSpark extends LocusWalkerSpark
See CollectAllelicCounts. This behaves the same, except that it supports spark.
See Also:

  • Constructor Details

    • CollectAllelicCountsSpark

      public CollectAllelicCountsSpark()

  • Method Details

    • emitEmptyLoci

      public boolean emitEmptyLoci()
      Description copied from class: LocusWalkerSpark
      Does this tool emit information for uncovered loci? Tools that do should override to return true. NOTE: Typically, this should only be used when intervals are specified. NOTE: If MappedReadFilter is removed, then emitting empty loci will fail. NOTE: If there is no available sequence dictionary and this is set to true, there should be a failure. Please consider requiring reads and/or references for all tools that wish to set this to true.
      Overrides:
      emitEmptyLoci in class LocusWalkerSpark
      Returns:
      true if this tool requires uncovered loci information to be emitted, false otherwise

    • requiresReference

      public boolean requiresReference()
      Description copied from class: GATKSparkTool
      Does this tool require reference data? Tools that do should override to return true.
      Overrides:
      requiresReference in class GATKSparkTool
      Returns:
      true if this tool requires a reference, otherwise false

    • requiresIntervals

      public boolean requiresIntervals()
      Description copied from class: GATKSparkTool
      Does this tool require intervals? Tools that do should override to return true.
      Overrides:
      requiresIntervals in class GATKSparkTool
      Returns:
      true if this tool requires intervals, otherwise false

    • getDefaultReadFilters

      public List<ReadFilter> getDefaultReadFilters()
      Description copied from class: GATKSparkTool
      Returns the default list of ReadFilters that are used for this tool. The filters returned by this method are subject to selective enabling/disabling by the user via the command line. The default implementation uses the WellformedReadFilter filter with all default options. Subclasses can override to provide alternative filters. Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is available through GATKSparkTool.getHeaderForReads(). The actual SAMFileHeader is propagated to the read filters by GATKSparkTool.makeReadFilter() after the filters have been merged with command line arguments.
      Overrides:
      getDefaultReadFilters in class GATKSparkTool
      Returns:
      List of individual filters to be applied for this tool.

    • processAlignments

      protected void processAlignments(org.apache.spark.api.java.JavaRDD<LocusWalkerContext> rdd, org.apache.spark.api.java.JavaSparkContext ctx)
      Description copied from class: LocusWalkerSpark
      Process the alignments and write output. Must be implemented by subclasses.
      Specified by:
      processAlignments in class LocusWalkerSpark
      Parameters:
      rdd - a distributed collection of LocusWalkerContext
      ctx - our Spark context