public class ExtractSequences extends CommandLineProgram
Modifier and Type | Field and Description |
---|---|
java.io.File |
INTERVAL_LIST |
int |
LINE_LENGTH |
java.io.File |
OUTPUT |
java.io.File |
REFERENCE_SEQUENCE |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
---|
ExtractSequences() |
Modifier and Type | Method and Description |
---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="Interval list describing intervals to be extracted from the reference sequence.") public java.io.File INTERVAL_LIST
@Option(shortName="R", doc="Reference sequence FASTA file.") public java.io.File REFERENCE_SEQUENCE
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram