picard.analysis.directed

Class CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>>

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.directed.CollectTargetedMetrics<METRIC,COLLECTOR>

Direct Known Subclasses:

CollectHsMetrics, CollectTargetedPcrMetrics

public abstract class CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>>
extends CommandLineProgram

Both CollectTargetedPCRMetrics and CalculateHybridSelection metrics share virtually identical program structures except for the name of their targeting mechanisms (e.g. bait set or amplicon set). The shared behavior of these programs is encapsulated in CollectTargetedMetrics which is then subclassed by CalculateHsMetrics and CollectTargetedPcrMetrics.

This program verifies the input parameters to TargetMetricsCollector and converts all files to the format desired by TargetMetricsCollector. Then it instantiates a TargetMetricsCollector and collects metric information for all reads in the INPUT sam file.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	CLIP_OVERLAPPING_READS
int	COVERAGE_CAP
java.io.File	INPUT
java.util.Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
int	MINIMUM_BASE_QUALITY
int	MINIMUM_MAPPING_QUALITY
int	NEAR_DISTANCE
java.io.File	OUTPUT
java.io.File	PER_BASE_COVERAGE
java.io.File	PER_TARGET_COVERAGE
int	SAMPLE_SIZE
java.util.List<java.io.File>	TARGET_INTERVALS

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectTargetedMetrics()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.
protected abstract htsjdk.samtools.util.IntervalList	getProbeIntervals()
protected abstract java.lang.String	getProbeSetName()
protected abstract COLLECTOR	makeCollector(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) A factory method for the TargetMetricsCollector to use this time.

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

TARGET_INTERVALS

@Option(shortName="TI",
        doc="An interval list file that contains the locations of the targets.",
        minElements=1)
public java.util.List<java.io.File> TARGET_INTERVALS

INPUT

@Option(shortName="I",
        doc="An aligned SAM or BAM file.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The output file to write the metrics to.")
public java.io.File OUTPUT

METRIC_ACCUMULATION_LEVEL

@Option(shortName="LEVEL",
        doc="The level(s) at which to accumulate metrics.")
public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

PER_TARGET_COVERAGE

@Option(optional=true,
        doc="An optional file to output per target coverage information to.")
public java.io.File PER_TARGET_COVERAGE

PER_BASE_COVERAGE

@Option(optional=true,
        doc="An optional file to output per base coverage information to. The per-base file contains one line per target base and can grow very large. It is not recommended for use with large target sets.")
public java.io.File PER_BASE_COVERAGE

NEAR_DISTANCE

@Option(optional=true,
        doc="The maximum distance between a read and the nearest probe/bait/amplicon for the read to be considered \'near probe\' and included in percent selected.")
public int NEAR_DISTANCE

MINIMUM_MAPPING_QUALITY

@Option(shortName="MQ",
        doc="Minimum mapping quality for a read to contribute coverage.",
        overridable=true)
public int MINIMUM_MAPPING_QUALITY

MINIMUM_BASE_QUALITY

@Option(shortName="Q",
        doc="Minimum base quality for a base to contribute coverage.",
        overridable=true)
public int MINIMUM_BASE_QUALITY

CLIP_OVERLAPPING_READS

@Option(doc="True if we are to clip overlapping reads, false otherwise.",
        optional=true,
        overridable=true)
public boolean CLIP_OVERLAPPING_READS

COVERAGE_CAP

@Option(shortName="covMax",
        doc="Parameter to set a max coverage limit for Theoretical Sensitivity calculations. Default is 200.",
        optional=true)
public int COVERAGE_CAP

SAMPLE_SIZE

@Option(doc="Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.",
        optional=true)
public int SAMPLE_SIZE

Constructor Detail

CollectTargetedMetrics

public CollectTargetedMetrics()

Method Detail

getProbeIntervals

protected abstract htsjdk.samtools.util.IntervalList getProbeIntervals()

getProbeSetName

protected abstract java.lang.String getProbeSetName()

makeCollector

protected abstract COLLECTOR makeCollector(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)

A factory method for the TargetMetricsCollector to use this time. Examples of TargetMetricsCollector: (TargetedPcrMetricsCollector, HsMetricsCalculator)

Returns:

A TargetMetricsCollector to which we will pass SAMRecords

doWork

protected int doWork()

Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.