picard.analysis.directed

Class CalculateHsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

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

picard.analysis.directed.CollectHsMetrics

picard.analysis.directed.CalculateHsMetrics

Deprecated.

@Deprecated
public class CalculateHsMetrics
extends CollectHsMetrics

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
boolean	CLIP_OVERLAPPING_READS Deprecated.
int	MINIMUM_BASE_QUALITY Deprecated.
int	MINIMUM_MAPPING_QUALITY Deprecated.

Fields inherited from class picard.analysis.directed.CollectHsMetrics

BAIT_INTERVALS, BAIT_SET_NAME

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
CalculateHsMetrics() Deprecated.

Method Summary

Methods inherited from class picard.analysis.directed.CollectHsMetrics

getProbeIntervals, getProbeSetName, main, makeCollector

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

MINIMUM_MAPPING_QUALITY

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

Deprecated.

MINIMUM_BASE_QUALITY

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

Deprecated.

CLIP_OVERLAPPING_READS

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

Deprecated.

Constructor Detail

CalculateHsMetrics

public CalculateHsMetrics()

Deprecated.