public class CollectWgsMetricsFromQuerySorted extends CommandLineProgram
Modifier and Type | Class and Description |
---|---|
static class |
CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
the various metrics types
|
static class |
CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
Metrics for evaluating the performance of whole genome sequencing experiments.
|
Modifier and Type | Field and Description |
---|---|
Long |
GENOME_TERRITORY |
File |
INPUT |
int |
MINIMUM_RAW_BASE_QUALITY |
int |
MINIMUM_RAW_MAPPING_QUALITY |
int |
MINIMUM_USABLE_BASE_QUALITY |
int |
MINIMUM_USABLE_MAPPING_QUALITY |
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 and Description |
---|
CollectWgsMetricsFromQuerySorted() |
Modifier and Type | Method and Description |
---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="USABLE_MQ", doc="Minimum mapping quality for a read to contribute to usable coverage.", overridable=true, optional=true) public int MINIMUM_USABLE_MAPPING_QUALITY
@Option(shortName="USABLE_Q", doc="Minimum base quality for a base to contribute to usable coverage.", overridable=true, optional=true) public int MINIMUM_USABLE_BASE_QUALITY
@Option(shortName="RAW_MQ", doc="Minimum mapping quality for a read to contribute to raw coverage.", overridable=true, optional=true) public int MINIMUM_RAW_MAPPING_QUALITY
@Option(shortName="RAW_Q", doc="Minimum base quality for a base to contribute to raw coverage.", overridable=true, optional=true) public int MINIMUM_RAW_BASE_QUALITY
@Option(doc="The number of bases in the genome build of the input file to be used for calculating MEAN_COVERAGE. If not provided, we will assume that ALL bases in the genome should be used (including e.g. Ns)", overridable=true, optional=true) public Long GENOME_TERRITORY
public static void main(String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram