@DocumentedFeature public final class CollectReadCounts extends ReadWalker
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.
format option
to TSV format. Using HDF5 files with CreateReadCountPanelOfNormals
can decrease runtime, by reducing time spent on IO, so this is the default output format.
The HDF5 format contains information in the paths defined in HDF5SimpleCountCollection. HDF5 files may be viewed using
hdfview or loaded in python using
PyTables or h5py.
The TSV format has a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in
SimpleCountCollection.SimpleCountTableColumn, and the corresponding entry rows.
gatk CollectReadCounts \
-I sample.bam \
-L intervals.interval_list \
--interval-merging-rule OVERLAPPING_ONLY \
-O sample.counts.hdf5
| Modifier and Type | Class and Description |
|---|---|
static class |
CollectReadCounts.Format |
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
FORMAT_LONG_NAME |
FEATURE_CACHE_LOOKAHEADaddOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArgumentsGATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
|---|
CollectReadCounts() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(GATKRead read,
ReferenceContext referenceContext,
FeatureContext featureContext)
Process an individual read (with optional contextual information).
|
java.util.List<ReadFilter> |
getDefaultReadFilters()
Returns the default list of CommandLineReadFilters that are used for this tool.
|
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 |
requiresIntervals()
Does this tool require intervals? Traversals types and/or tools that do should override to return true.
|
getProgressMeterRecordLabel, onShutdown, onStartup, requiresReads, resetReadsDataSource, traversedirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, requiresFeatures, requiresReference, transformTraversalIntervals, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatuspublic static final java.lang.String FORMAT_LONG_NAME
public boolean requiresIntervals()
GATKToolrequiresIntervals in class GATKToolpublic java.util.List<ReadFilter> getDefaultReadFilters()
ReadWalkerWellformedReadFilter 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 {link #getHeaderForReads}.getDefaultReadFilters in class ReadWalkerpublic void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(GATKRead read, ReferenceContext referenceContext, FeatureContext featureContext)
ReadWalkerapply in class ReadWalkerread - current readreferenceContext - Reference bases spanning the current read. Will be an empty, but non-null, context object
if there is no backing source of reference data (in which case all queries on it will return
an empty array/iterator). Can request extra bases of context around the current read's interval
by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()featureContext - Features spanning the current read. Will be an empty, but non-null, context object
if there is no backing source of Feature data (in which case all queries on it will return an
empty List).public java.lang.Object onTraversalSuccess()
GATKToolonTraversalSuccess in class GATKTool