picard.metrics

Class MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends java.lang.Comparable,ARGTYPE>

java.lang.Object

picard.metrics.MultiLevelCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>

Type Parameters:

METRIC_TYPE - The type of metrics being collected

Histogram_KEY - If there is are Histograms related to metrics of type then is the key value to these Histograms

ARGTYPE - The type of argument passed to individual PerUnitMetricCollector (see SAMRecordMultilevelCollector and PerUnitMetricCollector)

Direct Known Subclasses:

GcBiasMetricsCollector, InsertSizeMetricsCollector, SAMRecordAndReferenceMultiLevelCollector, SAMRecordMultiLevelCollector

public abstract class MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends java.lang.Comparable,ARGTYPE>
extends java.lang.Object

MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP). Based on the accumulationLevels and readGroup records passed to its constructor, MultiLevelCollector will instantiate the number of PerUnitMetricCollector's needed to generate metrics for each of the levels provided. To Use: Instantiate a MultiLevelCollector and call setup(see thoughts about extending MultiLevelCollector below) setup will create the underlying classes that will handle the accumulation level logic. Pass all reads you wish to collect data against to MultiLevelCollector via the acceptRecord method Call finish and use addAllLevelsToFile to add all of the metrics at each accumulation level to the given file. Extend MultiLevelCollector and implement makeArg and makeChildCollector You will most likely want to make a class that extends PerUnitMetricCollector. This class should do the work of keeping track of values for one specific "accumulation unit" (e.g. for one library, or for one read group depending on what levels you are accumulating at). If a record has any expensive calculations to be done (that don't need to be done differently depending on what sample/library/read group the read is for) then create a container class for the results of these calculations and pass this class as the ARGTYPE of both the PerUnitMetricCollector and MultiLevelCollector. You can then do these calculations in the makeArg method and they will only be done once per record.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	UNKNOWN

Constructor Summary

Constructors

Constructor and Description
MultiLevelCollector()

Method Summary

Modifier and Type	Method and Description
void	acceptRecord(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequence refSeq) Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
void	addAllLevelsToFile(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE,Histogram_KEY> file) Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
void	finish() Call finish on all PerUnitMetricCollectors
PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>	getAllReadsCollector() Get the PerUnitMetricCollector that collects reads for all levels
protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>	makeAllReadCollector()
protected abstract ARGTYPE	makeArg(htsjdk.samtools.SAMRecord samRec, htsjdk.samtools.reference.ReferenceSequence refSeq)
protected abstract PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>	makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup) Construct a PerUnitMetricCollector with the given arguments.
protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>	makeLibraryCollector(htsjdk.samtools.SAMReadGroupRecord rg)
protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>	makeReadGroupCollector(htsjdk.samtools.SAMReadGroupRecord rg)
protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>	makeSampleCollector(htsjdk.samtools.SAMReadGroupRecord rg)
protected void	setup(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords) Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor

Methods inherited from class java.lang.Object

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

Field Detail

UNKNOWN

public static final java.lang.String UNKNOWN

See Also:

Constant Field Values

Constructor Detail

MultiLevelCollector

public MultiLevelCollector()

Method Detail

makeArg

protected abstract ARGTYPE makeArg(htsjdk.samtools.SAMRecord samRec,
                                   htsjdk.samtools.reference.ReferenceSequence refSeq)

makeChildCollector

protected abstract PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE> makeChildCollector(java.lang.String sample,
                                                                                                java.lang.String library,
                                                                                                java.lang.String readGroup)

Construct a PerUnitMetricCollector with the given arguments.

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,Histogram_KEY,ARGTYPE> makeAllReadCollector()

makeSampleCollector

protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE> makeSampleCollector(htsjdk.samtools.SAMReadGroupRecord rg)

makeLibraryCollector

protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE> makeLibraryCollector(htsjdk.samtools.SAMReadGroupRecord rg)

makeReadGroupCollector

protected PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE> makeReadGroupCollector(htsjdk.samtools.SAMReadGroupRecord rg)

setup

protected void setup(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                     java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords)

Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor

Parameters:

accumulationLevels - PerUnitMetricCollectors will only be created for the levels identified by accumulationLevels

samRgRecords - PerUnitMetricCollectors will be created for each of the different samples, libraries, and readGroups found in the records depending on the accumulationLevels provided

acceptRecord

public void acceptRecord(htsjdk.samtools.SAMRecord record,
                         htsjdk.samtools.reference.ReferenceSequence refSeq)

Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record

finish

public void finish()

Call finish on all PerUnitMetricCollectors

getAllReadsCollector

public PerUnitMetricCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE> getAllReadsCollector()

Get the PerUnitMetricCollector that collects reads for all levels

addAllLevelsToFile

public void addAllLevelsToFile(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE,Histogram_KEY> file)

Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.