@DocumentedFeature @BetaFeature public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics
| Modifier and Type | Class | Description |
|---|---|---|
static class |
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage |
Metrics for evaluating the performance of whole genome sequencing experiments.
|
protected class |
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector |
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection, CollectWgsMetrics.WgsMetrics, CollectWgsMetrics.WgsMetricsCollector| Modifier and Type | Field | Description |
|---|---|---|
File |
CHART_OUTPUT |
COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, intervalArugmentCollection, INTERVALS, LOCUS_ACCUMULATION_CAP, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, OUTPUT, READ_LENGTH, SAMPLE_SIZE, STOP_AFTER, USE_FAST_ALGORITHMCOMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
CollectWgsMetricsWithNonZeroCoverage() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
protected CollectWgsMetrics.WgsMetrics |
generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals,
htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
double pctExcludedByMapq,
double pctExcludedByDupes,
double pctExcludedByPairing,
double pctExcludedByBaseq,
double pctExcludedByOverlap,
double pctExcludedByCapping,
double pctTotal,
int coverageCap,
htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram,
int sampleSize) |
|
protected CollectWgsMetrics.WgsMetricsCollector |
getCollector(int coverageCap,
htsjdk.samtools.util.IntervalList intervals) |
Creates
AbstractWgsMetricsCollector implementation according to {@link this#USE_FAST_ALGORITHM} value. |
protected htsjdk.samtools.SamReader |
getSamReader() |
Gets the SamReader from which records will be examined.
|
static void |
main(String[] args) |
getBasesExcludedBy, getIntervalsToExamine, getLocusIterator, getSamFileHeader, makeIntervalArgumentCollection, requiresReferencecustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser@Argument(shortName="CHART",
doc="A file (with .pdf extension) to write the chart to.")
public File CHART_OUTPUT
public CollectWgsMetricsWithNonZeroCoverage()
public static void main(String[] args)
protected htsjdk.samtools.SamReader getSamReader()
CollectWgsMetricsgetSamReader in class CollectWgsMetricsprotected int doWork()
CommandLineProgramdoWork in class CollectWgsMetricsprotected CollectWgsMetrics.WgsMetrics generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int sampleSize)
generateWgsMetrics in class CollectWgsMetricsprotected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
CollectWgsMetricsAbstractWgsMetricsCollector implementation according to {@link this#USE_FAST_ALGORITHM} value.getCollector in class CollectWgsMetricscoverageCap - the maximum depth/coverage to consider.intervals - the intervals over which metrics are collected.FastWgsMetricsCollector implementation,
otherwise default algorithm is used and CollectWgsMetrics.WgsMetricsCollector is returned.