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:

CalculateHsMetrics, 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
File	INPUT
Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
File	OUTPUT
File	PER_TARGET_COVERAGE
List<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

Methods

Modifier and Type	Method and Description
protected 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 IntervalList	getProbeIntervals()
protected abstract String	getProbeSetName()
protected abstract COLLECTOR	makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, ReferenceSequenceFile refFile, File perTargetCoverage, IntervalList targetIntervals, IntervalList probeIntervals, String probeSetName) 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 List<File> TARGET_INTERVALS

INPUT

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

OUTPUT

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

METRIC_ACCUMULATION_LEVEL

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

PER_TARGET_COVERAGE

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

Constructor Detail

CollectTargetedMetrics

public CollectTargetedMetrics()

Method Detail

getProbeIntervals

protected abstract IntervalList getProbeIntervals()

getProbeSetName

protected abstract String getProbeSetName()

makeCollector

protected abstract COLLECTOR makeCollector(Set<MetricAccumulationLevel> accumulationLevels,
                      List<SAMReadGroupRecord> samRgRecords,
                      ReferenceSequenceFile refFile,
                      File perTargetCoverage,
                      IntervalList targetIntervals,
                      IntervalList probeIntervals,
                      String probeSetName)

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 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.