public class FixVcfHeader extends CommandLineProgram
Modifier and Type | Field and Description |
---|---|
int |
CHECK_FIRST_N_RECORDS |
boolean |
ENFORCE_SAME_SAMPLES |
File |
HEADER |
File |
INPUT |
File |
OUTPUT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
---|
FixVcfHeader() |
Modifier and Type | Method and 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.
|
static void |
main(String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(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
public static void main(String[] args)
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram