picard.analysis.directed

Class CalculateHsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.directed.CollectTargetedMetrics<HsMetrics,HsMetricCollector>

picard.analysis.directed.CalculateHsMetrics

public class CalculateHsMetrics
extends CollectTargetedMetrics<HsMetrics,HsMetricCollector>

Calculates a set of HS metrics from a sam or bam file. See HsMetricsCollector and CollectTargetedMetrics for more details.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
List<File>	BAIT_INTERVALS
String	BAIT_SET_NAME

Fields inherited from class picard.analysis.directed.CollectTargetedMetrics

INPUT, METRIC_ACCUMULATION_LEVEL, OUTPUT, PER_TARGET_COVERAGE, 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
CalculateHsMetrics()

Method Summary

Methods

Modifier and Type	Method and Description
protected IntervalList	getProbeIntervals()
protected String	getProbeSetName()
static void	main(String[] argv) Stock main method.
protected HsMetricCollector	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.analysis.directed.CollectTargetedMetrics

customCommandLineValidation, doWork

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

BAIT_INTERVALS

@Option(shortName="BI",
        doc="An interval list file that contains the locations of the baits used.",
        minElements=1)
public List<File> BAIT_INTERVALS

BAIT_SET_NAME

@Option(shortName="N",
        doc="Bait set name. If not provided it is inferred from the filename of the bait intervals.",
        optional=true)
public String BAIT_SET_NAME

Constructor Detail

CalculateHsMetrics

public CalculateHsMetrics()

Method Detail

getProbeIntervals

protected IntervalList getProbeIntervals()

Specified by:

getProbeIntervals in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>

getProbeSetName

protected String getProbeSetName()

Specified by:

getProbeSetName in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>

main

public static void main(String[] argv)

Stock main method.

makeCollector

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

Description copied from class: CollectTargetedMetrics

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

Specified by:

makeCollector in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>

Returns:

A TargetMetricsCollector to which we will pass SAMRecords