public class CalculateHsMetrics extends CollectTargetedMetrics<HsMetrics,HsMetricCollector>
Modifier and Type | Field and Description |
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List<File> |
BAIT_INTERVALS |
String |
BAIT_SET_NAME |
INPUT, METRIC_ACCUMULATION_LEVEL, OUTPUT, PER_TARGET_COVERAGE, TARGET_INTERVALS
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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CalculateHsMetrics() |
Modifier and Type | Method and Description |
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protected IntervalList |
getProbeIntervals() |
protected String |
getProbeSetName() |
static void |
main(String[] argv)
Stock main method.
|
protected HsMetricCollector |
makeCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName)
A factory method for the TargetMetricsCollector to use this time.
|
customCommandLineValidation, doWork
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="BI", doc="An interval list file that contains the locations of the baits used.", minElements=1) public List<File> BAIT_INTERVALS
protected IntervalList getProbeIntervals()
getProbeIntervals
in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>
protected String getProbeSetName()
getProbeSetName
in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>
public static void main(String[] argv)
protected HsMetricCollector makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, ReferenceSequenceFile refFile, File perTargetCoverage, IntervalList targetIntervals, IntervalList probeIntervals, String probeSetName)
CollectTargetedMetrics
makeCollector
in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>