org.broadinstitute.hellbender.tools.spark.pipelines

Class CountReadsSpark

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.CountReadsSpark

All Implemented Interfaces:

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

@DocumentedFeature
public final class CountReadsSpark
extends GATKSparkTool

Calculate the overall number of reads in a SAM/BAM file

Input

• A single BAM file

Output

• A text file containing number of reads

Example

Output number of reads to file

   gatk CountReadsSpark \
     -I input_reads.bam \
     -O read_count.txt
 

Print read count

   gatk CountReadsSpark \
     -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
CountReadsSpark()

Method Summary

Modifier and Type	Method and Description
java.util.List<ReadFilter>	getDefaultReadFilters() Returns the default list of ReadFilters that are used for this tool.
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, 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

CountReadsSpark

public CountReadsSpark()

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

getDefaultReadFilters

public java.util.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.

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