picard.analysis.directed

Class TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>

java.lang.Object

picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>

picard.metrics.SAMRecordMultiLevelCollector<METRIC_TYPE,java.lang.Integer>

picard.analysis.directed.TargetMetricsCollector<METRIC_TYPE>

Direct Known Subclasses:

HsMetricCollector, TargetedPcrMetricsCollector

public abstract class TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
extends SAMRecordMultiLevelCollector<METRIC_TYPE,java.lang.Integer>

TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics. TargetMetricsCollector collects for a run these common metrics and can be sub-classed to provide metrics more specific to a targeted sequencing run. Note: Probe is the name I've used to indicate the bait set or amplicon set (e.g. the individual technological units used to target specific sites).

Author:

Jonathan Burke

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TargetMetricsCollector.Coverage A simple class that is used to store the coverage information about an interval.
class	TargetMetricsCollector.PerUnitTargetMetricCollector Collect the Target Metrics for one unit of "accumulation" (i.e.

Field Summary

Fields

Modifier and Type	Field and Description
static int	NEAR_PROBE_DISTANCE_DEFAULT Default distance for a read to be considered "selected".

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
TargetMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, java.io.File perTargetCoverage, java.io.File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, java.lang.String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean noSideEffects, int coverageCap, int sampleSize)
TargetMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, java.io.File perTargetCoverage, java.io.File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, java.lang.String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, int coverageCap, int sampleSize)

Method Summary

Modifier and Type	Method and Description
abstract METRIC_TYPE	convertMetric(picard.analysis.directed.TargetMetrics targetMetrics)
int	getNearProbeDistance() Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
static int	getNumBasesPassingMinimumBaseQuality(htsjdk.samtools.SAMRecord record, htsjdk.samtools.AlignmentBlock block, int minimumBaseQuality) Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
protected PerUnitMetricCollector<METRIC_TYPE,java.lang.Integer,htsjdk.samtools.SAMRecord>	makeAllReadCollector()
protected PerUnitMetricCollector<METRIC_TYPE,java.lang.Integer,htsjdk.samtools.SAMRecord>	makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup) Construct a PerUnitMetricCollector with the given arguments.
protected static <MT extends htsjdk.samtools.metrics.MetricBase> void	reflectiveCopy(picard.analysis.directed.TargetMetrics targetMetrics, MT outputMetrics, java.lang.String[] targetKeys, java.lang.String[] outputKeys) Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name.
void	setNearProbeDistance(int nearProbeDistance) Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
void	setNoSideEffects(boolean value) In the case of ignoring bases in overlapping reads from the same template, we choose to internally modify the SAM record's CIGAR to clip overlapping bases.

Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector

makeArg

Methods inherited from class picard.metrics.MultiLevelCollector

acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NEAR_PROBE_DISTANCE_DEFAULT

public static final int NEAR_PROBE_DISTANCE_DEFAULT

Default distance for a read to be considered "selected".

See Also:

Constant Field Values

Constructor Detail

TargetMetricsCollector

public TargetMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                              java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                              htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                              java.io.File perTargetCoverage,
                              java.io.File perBaseCoverage,
                              htsjdk.samtools.util.IntervalList targetIntervals,
                              htsjdk.samtools.util.IntervalList probeIntervals,
                              java.lang.String probeSetName,
                              int nearProbeDistance,
                              int minimumMappingQuality,
                              int minimumBaseQuality,
                              boolean clipOverlappingReads,
                              int coverageCap,
                              int sampleSize)

TargetMetricsCollector

public TargetMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                              java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                              htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                              java.io.File perTargetCoverage,
                              java.io.File perBaseCoverage,
                              htsjdk.samtools.util.IntervalList targetIntervals,
                              htsjdk.samtools.util.IntervalList probeIntervals,
                              java.lang.String probeSetName,
                              int nearProbeDistance,
                              int minimumMappingQuality,
                              int minimumBaseQuality,
                              boolean clipOverlappingReads,
                              boolean noSideEffects,
                              int coverageCap,
                              int sampleSize)

Method Detail

getNearProbeDistance

public int getNearProbeDistance()

Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.

setNearProbeDistance

public void setNearProbeDistance(int nearProbeDistance)

Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.

convertMetric

public abstract METRIC_TYPE convertMetric(picard.analysis.directed.TargetMetrics targetMetrics)

setNoSideEffects

public void setNoSideEffects(boolean value)

In the case of ignoring bases in overlapping reads from the same template, we choose to internally modify the SAM record's CIGAR to clip overlapping bases. We can either to modify the passed-in record (a side-effect), or modify a an internally clone of the record (no side-effect). Due to the overhead of cloning a SAMRecord object, we may see significant slow down of the performance to ensure there are no side effects. Therefore, users of this collector who do not care if the record passed to MultiLevelCollector.acceptRecord(htsjdk.samtools.SAMRecord, htsjdk.samtools.reference.ReferenceSequence) is modified can pass in false to this method to realize performance gains.

Parameters:

value - the boolean value to set.

getNumBasesPassingMinimumBaseQuality

public static int getNumBasesPassingMinimumBaseQuality(htsjdk.samtools.SAMRecord record,
                                                       htsjdk.samtools.AlignmentBlock block,
                                                       int minimumBaseQuality)

Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum

reflectiveCopy

protected static <MT extends htsjdk.samtools.metrics.MetricBase> void reflectiveCopy(picard.analysis.directed.TargetMetrics targetMetrics,
                                                                                     MT outputMetrics,
                                                                                     java.lang.String[] targetKeys,
                                                                                     java.lang.String[] outputKeys)

Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name. If no matching attribute exists in the outputMetrics or the attribute of the target metrics class also is found in targetKeys then it's value is not copied. Further more, targetKeys and outputKeys are attribute name arrays synchronized by the index. For each target key, targetMetrics. is assigned to outputMetrics.

Type Parameters:

MT - The type of metric of outputMetrics

Parameters:

targetMetrics - A metric with values to be copied

outputMetrics - A metrics intended to receive values from targetMetrics

targetKeys - Specific names of attributes of targetMetrics to copy to outputMetrics, each key has a corresponding one in outputKeys

outputKeys - Specific names of the destination attributes of outputMetrics that will be filled with values of outputMetrics, each key has a corresponding one in targetKeys

makeChildCollector

protected PerUnitMetricCollector<METRIC_TYPE,java.lang.Integer,htsjdk.samtools.SAMRecord> makeChildCollector(java.lang.String sample,
                                                                                                             java.lang.String library,
                                                                                                             java.lang.String readGroup)

Description copied from class: MultiLevelCollector

Construct a PerUnitMetricCollector with the given arguments.

Specified by:

makeChildCollector in class MultiLevelCollector<METRIC_TYPE extends MultilevelMetrics,java.lang.Integer,htsjdk.samtools.SAMRecord>

Parameters:

sample - If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collector

library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector

readGroup - If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector

Returns:

A PerUnitMetricCollector parameterized by the given arguments

makeAllReadCollector

protected PerUnitMetricCollector<METRIC_TYPE,java.lang.Integer,htsjdk.samtools.SAMRecord> makeAllReadCollector()

Overrides:

makeAllReadCollector in class MultiLevelCollector<METRIC_TYPE extends MultilevelMetrics,java.lang.Integer,htsjdk.samtools.SAMRecord>