Uses of Class
picard.filter.CountingFilter

Packages that use CountingFilter

Package	Description
picard.analysis
picard.filter

Uses of CountingFilter in picard.analysis

Methods in picard.analysis with parameters of type CountingFilter

Modifier and Type	Method and Description
protected void	CollectWgsMetrics.WgsMetricsCollector.addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
void	CollectWgsMetrics.WgsMetricsCollector.addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
void	CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector.addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
protected long	CollectWgsMetrics.getBasesExcludedBy(CountingFilter filter) If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge.
protected long	CollectWgsMetricsFromSampledSites.getBasesExcludedBy(CountingFilter filter) Deprecated. By design we want to count just those bases at the positions we care about, not across the entire read.
protected CollectWgsMetrics.WgsMetrics	CollectWgsMetrics.WgsMetricsCollector.getMetrics(htsjdk.samtools.util.Histogram<java.lang.Integer> depthHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)

Uses of CountingFilter in picard.filter

Subclasses of CountingFilter in picard.filter

Modifier and Type	Class and Description
class	CountingDuplicateFilter Counting filter that discards reads that have been marked as duplicates.
class	CountingMapQFilter Counting filter that discards reads below a configurable mapping quality threshold.
class	CountingPairedFilter Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.