Package picard.util
Class ScatterIntervalsByNs
java.lang.Object
picard.cmdline.CommandLineProgram
picard.util.ScatterIntervalsByNs
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
A reference file to use for creating the intervals
Which type of intervals to emit in the output (Ns only, ACGT only or both).
An integer indicating the largest number of Ns in a contiguous block that will be "tolerated" and not
converted into an N block.
An interval list (with a SAM header) where the names of the intervals are labeled (either N-block or ACGT-block) to indicate what type of block they define.
Summary
Used for creating a broken-up interval list that can be used for scattering a variant-calling pipeline in a way that will not cause problems at the edges of the intervals. By using large enough N blocks (so that the tools will not be able to anchor on both sides) we can be assured that the results of scattering and gathering the variants with the resulting interval list will be the same as calling with one large region.Input
Output
An interval list (with a SAM header) where the names of the intervals are labeled (either N-block or ACGT-block) to indicate what type of block they define.
Usage example
Create an interval list of intervals that do not contain any N blocks for use with haplotype caller on short reads
java -jar picard.jar ScatterIntervalsByNs \ R=reference_sequence.fasta \ OT=BOTH \ O=output.interval_list
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
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Field Summary
FieldsModifier and TypeFieldDescriptionint
picard.util.ScatterIntervalsByNs.OutputType
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.protected ReferenceArgumentCollection
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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OUTPUT
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OUTPUT_TYPE
@Argument(shortName="OT", doc="Type of intervals to output.", optional=true) public picard.util.ScatterIntervalsByNs.OutputType OUTPUT_TYPE -
MAX_TO_MERGE
@Argument(shortName="N", doc="Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval.", optional=true) public int MAX_TO_MERGE
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Constructor Details
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ScatterIntervalsByNs
public ScatterIntervalsByNs()
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Method Details
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makeReferenceArgumentCollection
- Overrides:
makeReferenceArgumentCollection
in classCommandLineProgram
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doWork
protected int 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 classCommandLineProgram
- Returns:
- program exit status.
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