public class CollectMultipleMetrics extends CommandLineProgram
Modifier and Type | Class and Description |
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static class |
CollectMultipleMetrics.Program |
static interface |
CollectMultipleMetrics.ProgramInterface |
Modifier and Type | Field and Description |
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boolean |
ASSUME_SORTED |
File |
DB_SNP |
String |
FILE_EXTENSION |
boolean |
INCLUDE_UNPAIRED |
File |
INPUT |
File |
INTERVALS |
Set<MetricAccumulationLevel> |
METRIC_ACCUMULATION_LEVEL |
String |
OUTPUT |
Set<CollectMultipleMetrics.Program> |
PROGRAM |
int |
STOP_AFTER |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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CollectMultipleMetrics() |
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.
|
int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
void |
setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface> programsToRun)
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones
available via enum.
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getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="If true (default), then the sort order in the header file will be ignored.", shortName="AS") public boolean ASSUME_SORTED
@Option(doc="Stop after processing N reads, mainly for debugging.") public int STOP_AFTER
@Option(shortName="LEVEL", doc="The level(s) at which to accumulate metrics.") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
@Option(shortName="EXT", doc="Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null", optional=true) public String FILE_EXTENSION
@Option(doc="Set of metrics programs to apply during the pass through the SAM file.") public Set<CollectMultipleMetrics.Program> PROGRAM
@Option(doc="An optional list of intervals to restrict analysis to. Only pertains to some of the PROGRAMs. Programs whose stand-alone CLP does not have an INTERVALS argument will silently ignore this argument.", optional=true) public File INTERVALS
@Option(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis by some PROGRAMs; PROGRAMs whose CLP doesn\'t allow for this argument will quietly ignore it.", optional=true) public File DB_SNP
@Option(shortName="UNPAIRED", doc="Include unpaired reads in CollectSequencingArtifactMetrics. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored in CollectSequencingArtifactMetrics.") public boolean INCLUDE_UNPAIRED
public static void main(String[] args)
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
public void setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface> programsToRun)
public int doWork()
CommandLineProgram
doWork
in class CommandLineProgram