public class CollectRawWgsMetrics extends CollectWgsMetrics
Modifier and Type | Class and Description |
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static class |
CollectRawWgsMetrics.RawWgsMetrics |
CollectWgsMetrics.WgsMetrics, CollectWgsMetrics.WgsMetricsCollector
Modifier and Type | Field and Description |
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int |
COVERAGE_CAP |
int |
LOCUS_ACCUMULATION_CAP |
int |
MINIMUM_BASE_QUALITY |
int |
MINIMUM_MAPPING_QUALITY |
COUNT_UNPAIRED, INCLUDE_BQ_HISTOGRAM, INPUT, INTERVALS, 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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CollectRawWgsMetrics() |
Modifier and Type | Method and Description |
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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) |
doWork, getBasesExcludedBy, getCollector, getIntervalsToExamine, getLocusIterator, getSamFileHeader, getSamReader, main
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="MQ", doc="Minimum mapping quality for a read to contribute coverage.") public int MINIMUM_MAPPING_QUALITY
@Option(shortName="Q", doc="Minimum base quality for a base to contribute coverage.") public int MINIMUM_BASE_QUALITY
@Option(shortName="CAP", doc="Treat bases with coverage exceeding this value as if they had coverage at this value.") public int COVERAGE_CAP
@Option(doc="At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low") public int LOCUS_ACCUMULATION_CAP
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)
generateWgsMetrics
in class CollectWgsMetrics