public class CollectRawWgsMetrics extends CollectWgsMetrics
Modifier and Type | Class and Description |
---|---|
static class |
CollectRawWgsMetrics.RawWgsMetrics |
CollectWgsMetrics.WgsMetrics
Modifier and Type | Field and Description |
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int |
COVERAGE_CAP |
int |
MINIMUM_BASE_QUALITY |
int |
MINIMUM_MAPPING_QUALITY |
INCLUDE_BQ_HISTOGRAM, INPUT, OUTPUT, REFERENCE_SEQUENCE, STOP_AFTER
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
---|
CollectRawWgsMetrics() |
Modifier and Type | Method and Description |
---|---|
protected CollectWgsMetrics.WgsMetrics |
generateWgsMetrics() |
doWork, main
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="MQ", doc="Minimum mapping quality for a read to contribute coverage.") public int MINIMUM_MAPPING_QUALITY
@Option(shortName="Q", doc="Minimum base quality for a base to contribute coverage.") public int MINIMUM_BASE_QUALITY
protected CollectWgsMetrics.WgsMetrics generateWgsMetrics()
generateWgsMetrics
in class CollectWgsMetrics