public abstract class CommandLineProgram extends Object
Modifier and Type | Field and Description |
---|---|
int |
COMPRESSION_LEVEL |
Boolean |
CREATE_INDEX |
boolean |
CREATE_MD5_FILE |
String |
GA4GH_CLIENT_SECRETS |
Integer |
MAX_RECORDS_IN_RAM |
Boolean |
QUIET |
File |
REFERENCE_SEQUENCE |
List<File> |
TMP_DIR |
ValidationStringency |
VALIDATION_STRINGENCY |
Log.LogLevel |
VERBOSITY |
Constructor and Description |
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CommandLineProgram() |
Modifier and Type | Method and Description |
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protected String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
|
protected abstract int |
doWork()
Do the work after command line has been parsed.
|
String |
getCommandLine() |
CommandLineParser |
getCommandLineParser() |
List<Header> |
getDefaultHeaders() |
protected <A extends MetricBase,B extends Comparable<?>> |
getMetricsFile()
Gets a MetricsFile with default headers already written into it.
|
Map<String,Object> |
getNestedOptions() |
Map<String,Object> |
getNestedOptionsForHelp() |
String |
getStandardUsagePreamble() |
String |
getVersion() |
int |
instanceMain(String[] argv) |
void |
instanceMainWithExit(String[] argv) |
protected boolean |
parseArgs(String[] argv) |
void |
setDefaultHeaders(List<Header> headers) |
@Option(doc="Control verbosity of logging.", common=true) public Log.LogLevel VERBOSITY
@Option(doc="Whether to suppress job-summary info on System.err.", common=true) public Boolean QUIET
@Option(doc="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.", common=true) public ValidationStringency VALIDATION_STRINGENCY
@Option(doc="Compression level for all compressed files created (e.g. BAM and GELI).", common=true) public int COMPRESSION_LEVEL
@Option(doc="When writing SAM files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort a SAM file, and increases the amount of RAM needed.", optional=true, common=true) public Integer MAX_RECORDS_IN_RAM
@Option(doc="Whether to create a BAM index when writing a coordinate-sorted BAM file.", common=true) public Boolean CREATE_INDEX
@Option(doc="Whether to create an MD5 digest for any BAM or FASTQ files created. ", common=true) public boolean CREATE_MD5_FILE
@Option(shortName="R", doc="Reference sequence file.", common=true, optional=true, overridable=true) public File REFERENCE_SEQUENCE
protected abstract int doWork()
public void instanceMainWithExit(String[] argv)
public int instanceMain(String[] argv)
protected String[] customCommandLineValidation()
protected boolean parseArgs(String[] argv)
protected <A extends MetricBase,B extends Comparable<?>> MetricsFile<A,B> getMetricsFile()
public String getStandardUsagePreamble()
public CommandLineParser getCommandLineParser()
public String getVersion()
public String getCommandLine()
public Map<String,Object> getNestedOptions()
public Map<String,Object> getNestedOptionsForHelp()