Package picard.util
Class IntervalListToBed
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.util.IntervalListToBed
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@DocumentedFeature public class IntervalListToBed extends CommandLineProgram
Trivially simple command line program to convert an IntervalList file to a BED file.
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Field Summary
Fields Modifier and Type Field Description File
INPUT
File
OUTPUT
int
SCORE
boolean
SORT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, 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 IntervalListToBed()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="Input IntervalList file.") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="Output BED file.") public File OUTPUT
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SCORE
@Argument(doc="The score, between 0-1000, to output for each interval in the BED file.") public int SCORE
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SORT
@Argument(doc="If true, sort the interval list prior to outputting as BED file.") public boolean SORT
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Method Detail
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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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