Package picard.analysis.artifacts
Class ConvertSequencingArtifactToOxoG
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
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@DocumentedFeature public class ConvertSequencingArtifactToOxoG extends CommandLineProgram
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Field Summary
Fields Modifier and Type Field Description File
BAIT_BIAS_IN
File
INPUT_BASE
File
OUTPUT_BASE
static String
OXOG_METRICS_EXT
File
OXOG_OUT
File
PRE_ADAPTER_IN
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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 ConvertSequencingArtifactToOxoG()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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OXOG_METRICS_EXT
public static final String OXOG_METRICS_EXT
- See Also:
- Constant Field Values
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INPUT_BASE
@Argument(shortName="I", doc="Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics). If this is not specified, you must specify PRE_ADAPTER_IN and BAIT_BIAS_IN", optional=true) public File INPUT_BASE
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PRE_ADAPTER_IN
@Argument(doc="The pre adapter details input file. Defaults to a filename based on the input basename", optional=true) public File PRE_ADAPTER_IN
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BAIT_BIAS_IN
@Argument(doc="The bait bias input file. Defaults to a filename based on the input basename", optional=true) public File BAIT_BIAS_IN
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OUTPUT_BASE
@Argument(shortName="O", doc="Basename for output OxoG metrics. Defaults to same basename as input metrics", optional=true) public File OUTPUT_BASE
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OXOG_OUT
@Argument(doc="File for the output OxoG metrics. Defaults to a filename based on the output basename", optional=true) public File OXOG_OUT
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Method Detail
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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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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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