Package picard.analysis
Class FastWgsMetricsCollector
java.lang.Object
picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
picard.analysis.FastWgsMetricsCollector
public class FastWgsMetricsCollector
extends AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
Class represents fast algorithm for collecting data from
AbstractLocusInfo
with a list of aligned EdgingRecordAndOffset
objects. According to the algorithm
we receive only two EdgingRecordAndOffset
objects for each alignment block of a read:
one for the start of block and one for the end. When meeting a EdgingRecordAndOffset
with type EdgingRecordAndOffset.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 a EdgingRecordAndOffset
with type EdgingRecordAndOffset.Type.END
,
the read name is removed from the map with names of processed reads.-
Field Summary
Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
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Constructor Summary
ConstructorsConstructorDescriptionFastWgsMetricsCollector
(CollectWgsMetrics collectWgsMetrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals) Creates a collector and initializes the inner data structures -
Method Summary
Modifier and TypeMethodDescriptionvoid
addInfo
(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.EdgingRecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN) Accumulates the data from AbstractLocusInfo in inner structuresMethods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, addToMetricsFile, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter
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Constructor Details
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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 Details
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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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