Package picard.vcf
Class AccumulateVariantCallingMetrics
- java.lang.Object
-
- picard.cmdline.CommandLineProgram
-
- picard.vcf.AccumulateVariantCallingMetrics
-
@DocumentedFeature public class AccumulateVariantCallingMetrics extends CommandLineProgram
Combines multiple Variant Calling Metrics files into a single file.
-
-
Field Summary
Fields Modifier and Type Field Description List<File>
INPUT
File
OUTPUT
-
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
-
-
Constructor Summary
Constructors Constructor Description AccumulateVariantCallingMetrics()
-
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, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
-
-
-
Field Detail
-
INPUT
@Argument(shortName="I", doc="Paths (except for the file extensions) of Variant Calling Metrics files to read and merge.", minElements=1) public List<File> INPUT
-
OUTPUT
@Argument(shortName="O", doc="Path (except for the file extension) of output metrics files to write.") public File OUTPUT
-
-
Method Detail
-
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.
-
-