org.broadinstitute.hellbender.tools.spark.pipelines

Class CountBasesSpark

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

org.broadinstitute.hellbender.engine.spark.GATKSparkTool

org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSpark

All Implemented Interfaces:

java.io.Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class CountBasesSpark
extends GATKSparkTool

Calculate the overall number of bases SAM/BAM/CRAM file

Input

• A single BAM file

Output

• A text file containing number of bases

Example

Output base count to file

   gatk CountBasesSpark \
     -I input_reads.bam \
     -O base_count.txt
 

Print base count

     gatk CountBasesSpark \
       -I input_reads.bam
 

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

GATKSparkTool.ReadInputMergingPolicy

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	out

Fields inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

addOutputVCFCommandLine, BAM_PARTITION_SIZE_LONG_NAME, bamPartitionSplitSize, CREATE_OUTPUT_BAM_SPLITTING_INDEX_LONG_NAME, createOutputBamIndex, createOutputBamSplittingIndex, createOutputVariantIndex, features, intervalArgumentCollection, NUM_REDUCERS_LONG_NAME, numReducers, OUTPUT_SHARD_DIR_LONG_NAME, readArguments, referenceArguments, sequenceDictionaryValidationArguments, SHARDED_OUTPUT_LONG_NAME, shardedOutput, shardedPartsDir, USE_NIO, useNio

Fields inherited from class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

programName, SPARK_PROGRAM_NAME_LONG_NAME, sparkArgs

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CountBasesSpark()

Method Summary

Modifier and Type	Method and Description
boolean	requiresReads() Does this tool require reads? Tools that do should override to return true.
protected void	runTool(org.apache.spark.api.java.JavaSparkContext ctx) Runs the tool itself after initializing and validating inputs.

Methods inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

addReferenceFilesForSpark, addVCFsForSpark, editIntervals, getBestAvailableSequenceDictionary, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGatkReadJavaRDD, getHeaderForReads, getIntervals, getPluginDescriptors, getReadInputMergingPolicy, getReads, getReadSourceHeaderMap, getReadSourceName, getRecommendedNumReducers, getReference, getReferenceSequenceDictionary, getReferenceWindowFunction, getSequenceDictionaryValidationArgumentCollection, getTargetPartitionSize, getUnfilteredReads, hasReads, hasReference, hasUserSuppliedIntervals, makeReadFilter, makeReadFilter, makeVariantAnnotations, requiresIntervals, requiresReference, runPipeline, useVariantAnnotations, validateSequenceDictionaries, writeReads, writeReads

Methods inherited from class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

afterPipeline, doWork, getProgramName

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, onStartup, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

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

Field Detail

out

@Argument(doc="uri for the output file: a local file path",
          shortName="O",
          fullName="output",
          optional=true)
public java.lang.String out

Constructor Detail

CountBasesSpark

public CountBasesSpark()

Method Detail

requiresReads

public boolean requiresReads()

Description copied from class: GATKSparkTool

Does this tool require reads? Tools that do should override to return true.

Overrides:

requiresReads in class GATKSparkTool

Returns:

true if this tool requires reads, otherwise false

runTool

protected void runTool(org.apache.spark.api.java.JavaSparkContext ctx)

Description copied from class: GATKSparkTool

Runs the tool itself after initializing and validating inputs. Must be implemented by subclasses.

Specified by:

runTool in class GATKSparkTool

Parameters:

ctx - our Spark context