Package picard.util
Class BedToIntervalList
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.util.BedToIntervalList
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@DocumentedFeature public class BedToIntervalList extends CommandLineProgram
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Field Summary
Fields Modifier and Type Field Description boolean
DROP_MISSING_CONTIGS
File
INPUT
File
OUTPUT
File
SEQUENCE_DICTIONARY
boolean
SORT
boolean
UNIQUE
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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 BedToIntervalList()
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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
checkRInstallation, 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="The input BED file") public File INPUT
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SEQUENCE_DICTIONARY
@Argument(shortName="SD", doc="The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.") public File SEQUENCE_DICTIONARY
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OUTPUT
@Argument(shortName="O", doc="The output Picard Interval List") public File OUTPUT
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SORT
@Argument(doc="If true, sort the output interval list before writing it.") public boolean SORT
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UNIQUE
@Argument(doc="If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).") public boolean UNIQUE
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DROP_MISSING_CONTIGS
@Hidden @Argument(doc="If true, entries that are on contig-names that are missing from the provided dictionary will be dropped.") public boolean DROP_MISSING_CONTIGS
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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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