org.broadinstitute.hellbender.tools.dragstr

Class DragstrHyperParameters

java.lang.Object

org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters

public final class DragstrHyperParameters
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	API_MONO_THRESHOLD_FULL_NAME
static java.lang.String	API_VALUES_ARGUMENT_FULL_NAME
static int	DEFAULT_API_MONO_THRESHOLD
static double	DEFAULT_HET_TO_HOM_RATIO
static int	DEFAULT_MAX_PERIOD
static int	DEFAULT_MAX_REPEAT_LENGTH
static int	DEFAULT_MIN_DEPTH
static int	DEFAULT_MIN_LOCI_COUNT
static DoubleSequence	DEFAULT_PHRED_API_VALUES
static DoubleSequence	DEFAULT_PHRED_GOP_VALUES
static DoubleSequence	DEFAULT_PHRED_GP_VALUES
static int	DEFAULT_SAMPLING_MIN_MQ
static int	DEFAULT_SAMPLING_PADDING
static java.lang.String	GOP_VALUES_ARGUMENT_FULL_NAME
static java.lang.String	GP_VALUES_ARGUMENT_FULL_NAME
static java.lang.String	HET_TO_HOM_RATIO_FULL_NAME
static java.lang.String	MAX_PERIOD_ARGUMENT_FULL_NAME
static java.lang.String	MAX_REPEATS_ARGUMENT_FULL_NAME
int	maxPeriod
int	maxRepeatLength
static java.lang.String	MIN_DEPTH_ARGUMENT_FULL_NAME
static java.lang.String	MIN_DEPTH_ARGUMENT_SHORT_NAME
static java.lang.String	MIN_LOCI_COUNT_FULL_NAME
int	minDepth
int	minMQ
static java.lang.String	SAMPLING_MIN_MQ_ARGUMENT_FULL_NAME
static java.lang.String	SAMPLING_PADDING_ARGUMENT_FULL_NAME
int	strPadding

Constructor Summary

Constructors

Constructor and Description
DragstrHyperParameters()

Method Summary

Modifier and Type	Method and Description
void	validate() Performs some validation constraint changes on the values provided to this argument collection.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAX_PERIOD

public static final int DEFAULT_MAX_PERIOD

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Constant Field Values

DEFAULT_MAX_REPEAT_LENGTH

public static final int DEFAULT_MAX_REPEAT_LENGTH

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Constant Field Values

DEFAULT_PHRED_GP_VALUES

public static final DoubleSequence DEFAULT_PHRED_GP_VALUES

GP_VALUES_ARGUMENT_FULL_NAME

public static final java.lang.String GP_VALUES_ARGUMENT_FULL_NAME

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Constant Field Values

DEFAULT_PHRED_API_VALUES

public static final DoubleSequence DEFAULT_PHRED_API_VALUES

API_VALUES_ARGUMENT_FULL_NAME

public static final java.lang.String API_VALUES_ARGUMENT_FULL_NAME

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Constant Field Values

DEFAULT_PHRED_GOP_VALUES

public static final DoubleSequence DEFAULT_PHRED_GOP_VALUES

GOP_VALUES_ARGUMENT_FULL_NAME

public static final java.lang.String GOP_VALUES_ARGUMENT_FULL_NAME

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Constant Field Values

DEFAULT_HET_TO_HOM_RATIO

public static final double DEFAULT_HET_TO_HOM_RATIO

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Constant Field Values

HET_TO_HOM_RATIO_FULL_NAME

public static final java.lang.String HET_TO_HOM_RATIO_FULL_NAME

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Constant Field Values

DEFAULT_MIN_LOCI_COUNT

public static final int DEFAULT_MIN_LOCI_COUNT

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Constant Field Values

MIN_LOCI_COUNT_FULL_NAME

public static final java.lang.String MIN_LOCI_COUNT_FULL_NAME

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Constant Field Values

DEFAULT_API_MONO_THRESHOLD

public static final int DEFAULT_API_MONO_THRESHOLD

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Constant Field Values

API_MONO_THRESHOLD_FULL_NAME

public static final java.lang.String API_MONO_THRESHOLD_FULL_NAME

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Constant Field Values

MAX_PERIOD_ARGUMENT_FULL_NAME

public static final java.lang.String MAX_PERIOD_ARGUMENT_FULL_NAME

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Constant Field Values

MAX_REPEATS_ARGUMENT_FULL_NAME

public static final java.lang.String MAX_REPEATS_ARGUMENT_FULL_NAME

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Constant Field Values

DEFAULT_MIN_DEPTH

public static final int DEFAULT_MIN_DEPTH

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Constant Field Values

MIN_DEPTH_ARGUMENT_SHORT_NAME

public static final java.lang.String MIN_DEPTH_ARGUMENT_SHORT_NAME

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Constant Field Values

MIN_DEPTH_ARGUMENT_FULL_NAME

public static final java.lang.String MIN_DEPTH_ARGUMENT_FULL_NAME

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Constant Field Values

DEFAULT_SAMPLING_PADDING

public static final int DEFAULT_SAMPLING_PADDING

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Constant Field Values

SAMPLING_PADDING_ARGUMENT_FULL_NAME

public static final java.lang.String SAMPLING_PADDING_ARGUMENT_FULL_NAME

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Constant Field Values

DEFAULT_SAMPLING_MIN_MQ

public static final int DEFAULT_SAMPLING_MIN_MQ

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Constant Field Values

SAMPLING_MIN_MQ_ARGUMENT_FULL_NAME

public static final java.lang.String SAMPLING_MIN_MQ_ARGUMENT_FULL_NAME

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Constant Field Values

maxPeriod

@Argument(fullName="max-period",
          doc="maximum period considered in STR analysis",
          optional=true,
          minValue=2.0,
          maxValue=10.0)
public int maxPeriod

maxRepeatLength

@Argument(fullName="max-repeats",
          doc="maximum repeat length (in repeated units) considered in STR analyses",
          optional=true,
          minValue=2.0,
          maxValue=100.0)
public int maxRepeatLength

minDepth

@Argument(fullName="minimum-depth",
          shortName="md",
          doc="Minimum coverage to consider a locus for sampling",
          optional=true)
public int minDepth

strPadding

@Argument(fullName="pileup-padding",
          doc="bases on either side of the repeat that are included in the STR pileup",
          optional=true)
public int strPadding

minMQ

@Argument(fullName="sampling-min-mq",
          doc="the minimum read mapping quality allowed in sampled loci. Any read with a lower MQ will result in discarding that locus",
          optional=true)
public int minMQ

Constructor Detail

DragstrHyperParameters

public DragstrHyperParameters()

Method Detail

validate

public void validate()

Performs some validation constraint changes on the values provided to this argument collection.

Will throw the appropriate user exception if it detects any inconsistency.