picard.analysis.directed

Class CollectHsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

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

picard.analysis.directed.CollectHsMetrics

Direct Known Subclasses:

CalculateHsMetrics

public class CollectHsMetrics
extends CollectTargetedMetrics<HsMetrics,HsMetricCollector>

Collects 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
java.util.List<java.io.File>	BAIT_INTERVALS
java.lang.String	BAIT_SET_NAME
boolean	CLIP_OVERLAPPING_READS
int	MINIMUM_BASE_QUALITY
int	MINIMUM_MAPPING_QUALITY

Fields inherited from class picard.analysis.directed.CollectTargetedMetrics

COVERAGE_CAP, INPUT, METRIC_ACCUMULATION_LEVEL, NEAR_DISTANCE, OUTPUT, PER_BASE_COVERAGE, PER_TARGET_COVERAGE, SAMPLE_SIZE, 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
CollectHsMetrics()

Method Summary

Modifier and Type	Method and Description
protected htsjdk.samtools.util.IntervalList	getProbeIntervals()
protected java.lang.String	getProbeSetName()
static void	main(java.lang.String[] argv) Stock main method.
protected HsMetricCollector	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.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 java.util.List<java.io.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 java.lang.String BAIT_SET_NAME

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

Constructor Detail

CollectHsMetrics

public CollectHsMetrics()

Method Detail

getProbeIntervals

protected htsjdk.samtools.util.IntervalList getProbeIntervals()

Specified by:

getProbeIntervals in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>

getProbeSetName

protected java.lang.String getProbeSetName()

Specified by:

getProbeSetName in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>

main

public static void main(java.lang.String[] argv)

Stock main method.

makeCollector

protected HsMetricCollector 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)

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