public abstract class CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>> extends CommandLineProgram
Modifier and Type | Field and Description |
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File |
INPUT |
Set<MetricAccumulationLevel> |
METRIC_ACCUMULATION_LEVEL |
File |
OUTPUT |
File |
PER_TARGET_COVERAGE |
List<File> |
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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CollectTargetedMetrics() |
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.
|
protected int |
doWork()
Asserts that files are readable and writable and then fires off an
HsMetricsCalculator instance to do the real work.
|
protected abstract IntervalList |
getProbeIntervals() |
protected abstract String |
getProbeSetName() |
protected abstract COLLECTOR |
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.
|
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="TI", doc="An interval list file that contains the locations of the targets.", minElements=1) public List<File> TARGET_INTERVALS
@Option(shortName="LEVEL", doc="The level(s) at which to accumulate metrics.") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
protected abstract IntervalList getProbeIntervals()
protected abstract String getProbeSetName()
protected abstract COLLECTOR makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, ReferenceSequenceFile refFile, File perTargetCoverage, IntervalList targetIntervals, IntervalList probeIntervals, String probeSetName)
protected int doWork()
doWork
in class CommandLineProgram
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram