public class BuildBamIndex extends CommandLineProgram
Modifier and Type | Field | Description |
---|---|---|
String |
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 | Description |
---|---|
BuildBamIndex() |
Modifier and Type | Method | Description |
---|---|---|
protected int |
doWork() |
Main method for the program.
|
static void |
main(String[] argv) |
Stock main method for a command line program.
|
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="I", doc="A BAM file or GA4GH URL to process. Must be sorted in coordinate order.") public String INPUT
public static void main(String[] argv)
protected int doWork()
doWork
in class CommandLineProgram