Package picard.vcf
Class FixVcfHeader
- java.lang.Object
-
- picard.cmdline.CommandLineProgram
-
- picard.vcf.FixVcfHeader
-
@DocumentedFeature public class FixVcfHeader extends CommandLineProgram
Tool for replacing or fixing up a VCF header.
-
-
Field Summary
Fields Modifier and Type Field Description int
CHECK_FIRST_N_RECORDS
boolean
ENFORCE_SAME_SAMPLES
File
HEADER
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 FixVcfHeader()
-
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
-
-
-
-
Field Detail
-
INPUT
@Argument(shortName="I", doc="The input VCF/BCF file.") public File INPUT
-
OUTPUT
@Argument(shortName="O", doc="The output VCF/BCF file.") public File OUTPUT
-
CHECK_FIRST_N_RECORDS
@Argument(shortName="N", doc="Check only the first N records when searching for missing INFO and FORMAT fields.", optional=true) public int CHECK_FIRST_N_RECORDS
-
HEADER
@Argument(shortName="H", doc="The replacement VCF header.", optional=true) public File HEADER
-
ENFORCE_SAME_SAMPLES
@Argument(doc="Enforce that the samples are the same (and in the same order) when replacing the VCF header.", optional=true) public boolean ENFORCE_SAME_SAMPLES
-
-
Method Detail
-
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.
-
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.
-
-