org.broadinstitute.hellbender.tools

Class ConvertHeaderlessHadoopBamShardToBam

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
 @BetaFeature
public final class ConvertHeaderlessHadoopBamShardToBam
extends CommandLineProgram

This is a troubleshooting utility that converts a headerless BAM shard (e.g., a part-r-00000.bam, part-r-00001.bam, etc.), produced by a Spark tool with --sharded-output set to true, into a readable BAM file by adding a header and a BGZF terminator.

This tool is not intended for use with BAM shards that already have a header -- these shards are already readable using samtools.

Input

• A headerless BAM shard
• A well-formed BAM whose header will be used for the converted fragment

Output

• The converted BAM shard

Usage example

 gatk ConvertHeaderlessHadoopBamShardToBam \
     --bam-shard part-r-00000.bam \
     --bam-with-header input.bam \
     -O output.bam
 

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BAM_SHARD_LONG_NAME
static java.lang.String	BAM_WITH_HEADER_LONG_NAME
static java.lang.String	OUTPUT_LONG_NAME
static java.lang.String	OUTPUT_SHORT_NAME

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
ConvertHeaderlessHadoopBamShardToBam()

Method Summary

Modifier and Type	Method and Description
protected java.lang.Object	doWork() Do the work after command line has been parsed.

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, 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

BAM_SHARD_LONG_NAME

public static final java.lang.String BAM_SHARD_LONG_NAME

See Also:

Constant Field Values

BAM_WITH_HEADER_LONG_NAME

public static final java.lang.String BAM_WITH_HEADER_LONG_NAME

See Also:

Constant Field Values

OUTPUT_LONG_NAME

public static final java.lang.String OUTPUT_LONG_NAME

See Also:

Constant Field Values

OUTPUT_SHORT_NAME

public static final java.lang.String OUTPUT_SHORT_NAME

See Also:

Constant Field Values

Constructor Detail

ConvertHeaderlessHadoopBamShardToBam

public ConvertHeaderlessHadoopBamShardToBam()

Method Detail

doWork

protected java.lang.Object doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

the return value or null is there is none.