Package picard.analysis
Class FastWgsMetricsCollector
- java.lang.Object
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- picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
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- picard.analysis.FastWgsMetricsCollector
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public class FastWgsMetricsCollector extends AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
Class represents fast algorithm for collecting data fromAbstractLocusInfo
with a list of alignedEdgingRecordAndOffset
objects. According to the algorithm we receive only twoEdgingRecordAndOffset
objects for each alignment block of a read: one for the start of block and one for the end. When meeting aEdgingRecordAndOffset
with typeEdgingRecordAndOffset.Type.BEGIN
, all information from the alignment block is accumulated in the collector, read name is added to a map holding the names of processed reads for detecting overlapping positions. When meeting aEdgingRecordAndOffset
with typeEdgingRecordAndOffset.Type.END
, the read name is removed from the map with names of processed reads.
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Field Summary
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Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
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Constructor Summary
Constructors Constructor Description FastWgsMetricsCollector(CollectWgsMetrics collectWgsMetrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
Creates a collector and initializes the inner data structures
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.EdgingRecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)
Accumulates the data from AbstractLocusInfo in inner structures-
Methods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, addToMetricsFile, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter
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Constructor Detail
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FastWgsMetricsCollector
public FastWgsMetricsCollector(CollectWgsMetrics collectWgsMetrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
Creates a collector and initializes the inner data structures- Parameters:
collectWgsMetrics
- CollectWgsMetrics, that creates this collectorcoverageCap
- coverage cap
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Method Detail
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addInfo
public void addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.EdgingRecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)
Description copied from class:AbstractWgsMetricsCollector
Accumulates the data from AbstractLocusInfo in inner structures- Specified by:
addInfo
in classAbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
- Parameters:
info
-AbstractLocusInfo
with aligned to reference position readsref
-ReferenceSequence
referenceBaseN
- true if current the value of reference base represents a no call
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