public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics
Modifier and Type | Class and Description |
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static class |
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
Metrics for evaluating the performance of whole genome sequencing experiments.
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protected class |
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector |
CollectWgsMetrics.WgsMetrics, CollectWgsMetrics.WgsMetricsCollector
Modifier and Type | Field and Description |
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File |
CHART_OUTPUT |
COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, INTERVALS, LOCUS_ACCUMULATION_CAP, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, OUTPUT, REFERENCE_SEQUENCE, SAMPLE_SIZE, 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 |
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CollectWgsMetricsWithNonZeroCoverage() |
Modifier and Type | Method and Description |
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protected int |
doWork()
Do the work after command line has been parsed.
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protected CollectWgsMetrics.WgsMetrics |
generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals,
htsjdk.samtools.util.Histogram<Integer> depthHistogram,
double pctExcludedByMapq,
double pctExcludedByDupes,
double pctExcludedByPairing,
double pctExcludedByBaseq,
double pctExcludedByOverlap,
double pctExcludedByCapping,
double pctTotal,
int coverageCap,
htsjdk.samtools.util.Histogram<Integer> baseQHistogram,
int sampleSize) |
protected CollectWgsMetrics.WgsMetricsCollector |
getCollector(int coverageCap,
htsjdk.samtools.util.IntervalList intervals) |
protected htsjdk.samtools.SamReader |
getSamReader()
Gets the SamReader from which records will be examined.
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static void |
main(String[] args) |
getBasesExcludedBy, getIntervalsToExamine, getLocusIterator, getSamFileHeader
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
public CollectWgsMetricsWithNonZeroCoverage()
public static void main(String[] args)
protected htsjdk.samtools.SamReader getSamReader()
CollectWgsMetrics
getSamReader
in class CollectWgsMetrics
protected int doWork()
CommandLineProgram
doWork
in class CollectWgsMetrics
protected CollectWgsMetrics.WgsMetrics generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> depthHistogram, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> baseQHistogram, int sampleSize)
generateWgsMetrics
in class CollectWgsMetrics
protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
getCollector
in class CollectWgsMetrics
coverageCap
- the maximum depth/coverage to consider.intervals
- the intervals over which metrics are collected.