@DocumentedFeature 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, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, 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, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="A BAM file or GA4GH URL to process. Must be sorted in coordinate order.")
public String INPUT
@Argument(shortName="O",
doc="The BAM index file. Defaults to x.bai if INPUT is x.bam, otherwise INPUT.bai.\nIf INPUT is a URL and OUTPUT is unspecified, defaults to a file in the current directory.",
optional=true)
public File OUTPUT
public static void main(String[] argv)
protected int doWork()
doWork in class CommandLineProgram