public class CollectTargetedPcrMetrics extends CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>
Modifier and Type | Field and Description |
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java.io.File |
AMPLICON_INTERVALS |
java.lang.String |
CUSTOM_AMPLICON_SET_NAME |
CLIP_OVERLAPPING_READS, COVERAGE_CAP, INPUT, METRIC_ACCUMULATION_LEVEL, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, NEAR_DISTANCE, OUTPUT, PER_BASE_COVERAGE, PER_TARGET_COVERAGE, SAMPLE_SIZE, 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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CollectTargetedPcrMetrics() |
Modifier and Type | Method and Description |
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protected htsjdk.samtools.util.IntervalList |
getProbeIntervals() |
protected java.lang.String |
getProbeSetName() |
static void |
main(java.lang.String[] argv)
Stock main method.
|
protected TargetedPcrMetricsCollector |
makeCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
htsjdk.samtools.reference.ReferenceSequenceFile refFile,
java.io.File perTargetCoverage,
java.io.File perBaseCoverage,
htsjdk.samtools.util.IntervalList targetIntervals,
htsjdk.samtools.util.IntervalList probeIntervals,
java.lang.String probeSetName,
int nearProbeDistance)
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="AI", doc="An interval list file that contains the locations of the baits used.") public java.io.File AMPLICON_INTERVALS
protected htsjdk.samtools.util.IntervalList getProbeIntervals()
getProbeIntervals
in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>
protected java.lang.String getProbeSetName()
getProbeSetName
in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>
public static void main(java.lang.String[] argv)
protected TargetedPcrMetricsCollector makeCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, java.io.File perTargetCoverage, java.io.File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, java.lang.String probeSetName, int nearProbeDistance)
CollectTargetedMetrics
makeCollector
in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>