Package picard.sam
Class AddOATag
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.AddOATag
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@DocumentedFeature public class AddOATag extends CommandLineProgram
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Field Summary
Fields Modifier and Type Field Description String
INPUT
File
INTERVAL_LIST
String
OUTPUT
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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 AddOATag()
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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="SAM or BAM input file") public String INPUT
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OUTPUT
@Argument(shortName="O", doc="SAM or BAM file to write merged result to") public String OUTPUT
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INTERVAL_LIST
@Argument(shortName="L", doc="If provided, only records that overlap given interval list will have the OA tag added.", optional=true) public File INTERVAL_LIST
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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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