Package picard.util
Class ScatterIntervalsByNs
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.util.ScatterIntervalsByNs
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@DocumentedFeature public class ScatterIntervalsByNs extends CommandLineProgram
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
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
- 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.
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 Classes Modifier and Type Class Description static class
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
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Field Summary
Fields Modifier and Type Field Description int
MAX_TO_MERGE
File
OUTPUT
picard.util.ScatterIntervalsByNs.OutputType
OUTPUT_TYPE
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description ScatterIntervalsByNs()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.static void
main(String[] args)
protected ReferenceArgumentCollection
makeReferenceArgumentCollection()
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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OUTPUT
@Argument(shortName="O", doc="Output file for interval list.") public File 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
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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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Method Detail
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main
public static void main(String[] args)
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makeReferenceArgumentCollection
protected ReferenceArgumentCollection 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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