@Deprecated public class CollectWgsMetricsFromSampledSites extends CollectWgsMetrics
Modifier and Type | Class and Description |
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static class |
CollectWgsMetricsFromSampledSites.SampledWgsMetrics
Deprecated.
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CollectWgsMetrics.WgsMetrics, CollectWgsMetrics.WgsMetricsCollector
Modifier and Type | Field and Description |
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File |
INTERVALS
Deprecated.
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COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, 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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CollectWgsMetricsFromSampledSites()
Deprecated.
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Modifier and Type | Method and Description |
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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)
Deprecated.
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protected long |
getBasesExcludedBy(CountingFilter filter)
Deprecated.
By design we want to count just those bases at the positions we care about, not across the entire read.
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protected htsjdk.samtools.util.SamLocusIterator |
getLocusIterator(htsjdk.samtools.SamReader in)
Deprecated.
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static void |
main(String[] args)
Deprecated.
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doWork, getCollector, getIntervalsToExamine, getSamFileHeader, getSamReader
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
public CollectWgsMetricsFromSampledSites()
public static void main(String[] args)
protected htsjdk.samtools.util.SamLocusIterator getLocusIterator(htsjdk.samtools.SamReader in)
getLocusIterator
in class CollectWgsMetrics
protected long getBasesExcludedBy(CountingFilter filter)
getBasesExcludedBy
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