public abstract class CommandLineProgram
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
COMPRESSION_LEVEL |
java.lang.Boolean |
CREATE_INDEX |
boolean |
CREATE_MD5_FILE |
java.lang.String |
GA4GH_CLIENT_SECRETS |
java.lang.Integer |
MAX_RECORDS_IN_RAM |
java.lang.Boolean |
QUIET |
java.io.File |
REFERENCE_SEQUENCE |
java.util.List<java.io.File> |
TMP_DIR |
htsjdk.samtools.ValidationStringency |
VALIDATION_STRINGENCY |
htsjdk.samtools.util.Log.LogLevel |
VERBOSITY |
Constructor and Description |
---|
CommandLineProgram() |
Modifier and Type | Method and Description |
---|---|
protected java.lang.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.
|
java.lang.String |
getCommandLine() |
CommandLineParser |
getCommandLineParser() |
java.util.List<htsjdk.samtools.metrics.Header> |
getDefaultHeaders() |
protected <A extends htsjdk.samtools.metrics.MetricBase,B extends java.lang.Comparable<?>> |
getMetricsFile()
Gets a MetricsFile with default headers already written into it.
|
java.util.Map<java.lang.String,java.lang.Object> |
getNestedOptions() |
java.util.Map<java.lang.String,java.lang.Object> |
getNestedOptionsForHelp() |
java.lang.String |
getStandardUsagePreamble() |
java.lang.String |
getVersion() |
int |
instanceMain(java.lang.String[] argv) |
void |
instanceMainWithExit(java.lang.String[] argv) |
protected boolean |
parseArgs(java.lang.String[] argv) |
void |
setDefaultHeaders(java.util.List<htsjdk.samtools.metrics.Header> headers) |
@Option(doc="Control verbosity of logging.", common=true) public htsjdk.samtools.util.Log.LogLevel VERBOSITY
@Option(doc="Whether to suppress job-summary info on System.err.", common=true) public java.lang.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 htsjdk.samtools.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 java.lang.Integer MAX_RECORDS_IN_RAM
@Option(doc="Whether to create a BAM index when writing a coordinate-sorted BAM file.", common=true) public java.lang.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 java.io.File REFERENCE_SEQUENCE
protected abstract int doWork()
public void instanceMainWithExit(java.lang.String[] argv)
public int instanceMain(java.lang.String[] argv)
protected java.lang.String[] customCommandLineValidation()
protected boolean parseArgs(java.lang.String[] argv)
protected <A extends htsjdk.samtools.metrics.MetricBase,B extends java.lang.Comparable<?>> htsjdk.samtools.metrics.MetricsFile<A,B> getMetricsFile()
public java.lang.String getStandardUsagePreamble()
public CommandLineParser getCommandLineParser()
public java.lang.String getVersion()
public java.lang.String getCommandLine()
public void setDefaultHeaders(java.util.List<htsjdk.samtools.metrics.Header> headers)
public java.util.List<htsjdk.samtools.metrics.Header> getDefaultHeaders()
public java.util.Map<java.lang.String,java.lang.Object> getNestedOptions()
public java.util.Map<java.lang.String,java.lang.Object> getNestedOptionsForHelp()