org.broadinstitute.hellbender.tools.copynumber

Class PreprocessIntervals

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class PreprocessIntervals
extends GATKTool

Prepares bins for coverage collection.

The input intervals are first checked for overlapping intervals, which are merged. The resulting intervals are then padded. The padded intervals are then split into bins. Finally, bins that contain only Ns are filtered out.

Inputs

• Reference FASTA file
• Intervals to be preprocessed. The argument interval-merging-rule must be set to IntervalMergingRule.OVERLAPPING_ONLY and all other common arguments for interval padding or merging must be set to their defaults. If no intervals are specified, then each contig will be assumed to be a single interval and binned accordingly; this produces bins appropriate for whole genome sequencing analyses.
• Padding length (in bp). Use padding to specify the size of each of the regions added to both ends of the intervals that result after overlapping intervals have been merged. Do not use the common interval-padding argument. Intervals that would overlap after padding by the specified amount are instead only padded until they are adjacent.
• Bin length (in bp). If this length is not commensurate with the length of a padded interval, then the last bin will be of different length than the others in that interval. If zero is specified, then no binning will be performed; this is generally appropriate for targeted analyses.

Output

• Preprocessed Picard interval-list file.

Usage examples

To pad intervals by 250 bases and disable binning (e.g., for targeted analyses):

     gatk PreprocessIntervals \
          -R reference.fa \
          -L intervals.interval_list \
          --bin-length 0 \
          --padding 250 \
          -O preprocessed_intervals.interval_list
 

To generate consecutive bins of 1000 bases from the reference (e.g., for whole genome sequencing analyses):

     gatk PreprocessIntervals \
          -R reference.fa \
          --bin-length 1000 \
          --padding 0 \
          -O preprocessed_intervals.interval_list
 

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BIN_LENGTH_LONG_NAME
static java.lang.String	PADDING_LONG_NAME

Fields inherited from class org.broadinstitute.hellbender.engine.GATKTool

addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArguments

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
PreprocessIntervals()

Method Summary

Modifier and Type	Method and Description
void	onTraversalStart() Operations performed just prior to the start of traversal.
java.lang.Object	onTraversalSuccess() Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
boolean	requiresReference() Does this tool require reference data? Traversals types and/or tools that do should override to return true.
void	traverse() A complete traversal from start to finish.

Methods inherited from class org.broadinstitute.hellbender.engine.GATKTool

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getProgressMeterRecordLabel, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onShutdown, onStartup, requiresFeatures, requiresIntervals, requiresReads, transformTraversalIntervals, useVariantAnnotations

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, 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

BIN_LENGTH_LONG_NAME

public static final java.lang.String BIN_LENGTH_LONG_NAME

See Also:

Constant Field Values

PADDING_LONG_NAME

public static final java.lang.String PADDING_LONG_NAME

See Also:

Constant Field Values

Constructor Detail

PreprocessIntervals

public PreprocessIntervals()

Method Detail

requiresReference

public boolean requiresReference()

Description copied from class: GATKTool

Does this tool require reference data? Traversals types and/or tools that do should override to return true.

Overrides:

requiresReference in class GATKTool

Returns:

true if this tool requires a reference, otherwise false

onTraversalStart

public void onTraversalStart()

Description copied from class: GATKTool

Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.

Overrides:

onTraversalStart in class GATKTool

traverse

public void traverse()

Description copied from class: GATKTool

A complete traversal from start to finish. Tool authors who wish to "roll their own" traversal from scratch can extend this class directly and implement this method. Walker authors should instead extend a Walker class and implement the Walker-appropriate apply() method, since the Walker base classes implement the various kinds of traversals for you.

Specified by:

traverse in class GATKTool

onTraversalSuccess

public java.lang.Object onTraversalSuccess()

Description copied from class: GATKTool

Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal). Should be overridden by tool authors who need to close local resources, etc., after traversal. Also allows tools to return a value representing the traversal result, which is printed by the engine. Default implementation does nothing and returns null.

Overrides:

onTraversalSuccess in class GATKTool

Returns:

Object representing the traversal result, or null if a tool does not return a value