public class VcfToIntervalList extends CommandLineProgram
Modifier and Type | Field and Description |
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java.io.File |
INPUT |
static htsjdk.samtools.util.Log |
LOG |
java.io.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 |
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VcfToIntervalList() |
Modifier and Type | Method and Description |
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protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
public static final htsjdk.samtools.util.Log LOG
@Option(doc="The BCF or VCF input file. The file format is determined by file extension.", shortName="I") public java.io.File INPUT
public static void main(java.lang.String[] argv)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram