org.broadinstitute.hellbender.tools.walkers.vqsr

Class Tranche

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche

Direct Known Subclasses:

VQSLODTranche

public class Tranche
extends java.lang.Object

Created by gauthier on 7/13/17.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Tranche.TrancheComparator<T extends Tranche>
static class	Tranche.TrancheTruthSensitivityComparator

Field Summary

Fields

Modifier and Type	Field and Description
protected int	accessibleTruthSites
protected int	callsAtTruthSites
protected static java.lang.String	COMMENT_STRING
protected static java.lang.String	DEFAULT_TRANCHE_NAME
protected static int	EXPECTED_COLUMN_COUNT
protected static java.lang.String	VALUE_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
Tranche(java.lang.String name, double knownTiTv, int numNovel, double minVQSLod, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model, double novelTiTv, int accessibleTruthSites, int numKnown, int callsAtTruthSites)

Method Summary

Modifier and Type	Method and Description
protected static Tranche	emptyTranche(java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum> data, int minI, double ts, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model)
protected static double	getOptionalDouble(java.util.Map<java.lang.String,java.lang.String> bindings, java.lang.String key, double defaultValue)
protected static int	getOptionalInteger(java.util.Map<java.lang.String,java.lang.String> bindings, java.lang.String key, int defaultValue)
protected static double	getRequiredDouble(java.util.Map<java.lang.String,java.lang.String> bindings, java.lang.String key)
protected static int	getRequiredInteger(java.util.Map<java.lang.String,java.lang.String> bindings, java.lang.String key)
java.lang.Double	getTrancheIndex()
<T extends Tranche> java.lang.String	getTrancheString(T prev)
protected double	getTruthSensitivity()
protected static Tranche	trancheOfVariants(java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum> data, int minI, double ts, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model)
static java.lang.String	tranchesString(java.util.List<? extends Tranche> tranches) Returns an appropriately formatted string representing the raw tranches file on disk.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_TRANCHE_NAME

protected static final java.lang.String DEFAULT_TRANCHE_NAME

See Also:

Constant Field Values

COMMENT_STRING

protected static final java.lang.String COMMENT_STRING

See Also:

Constant Field Values

VALUE_SEPARATOR

protected static final java.lang.String VALUE_SEPARATOR

See Also:

Constant Field Values

EXPECTED_COLUMN_COUNT

protected static final int EXPECTED_COLUMN_COUNT

See Also:

Constant Field Values

accessibleTruthSites

protected final int accessibleTruthSites

callsAtTruthSites

protected final int callsAtTruthSites

Constructor Detail

Tranche

public Tranche(java.lang.String name,
               double knownTiTv,
               int numNovel,
               double minVQSLod,
               org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model,
               double novelTiTv,
               int accessibleTruthSites,
               int numKnown,
               int callsAtTruthSites)

Method Detail

tranchesString

public static java.lang.String tranchesString(java.util.List<? extends Tranche> tranches)

Returns an appropriately formatted string representing the raw tranches file on disk.

Parameters:

tranches -

Returns:

getTrancheIndex

public java.lang.Double getTrancheIndex()

getTrancheString

public <T extends Tranche> java.lang.String getTrancheString(T prev)

trancheOfVariants

protected static Tranche trancheOfVariants(java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum> data,
                                           int minI,
                                           double ts,
                                           org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model)

emptyTranche

protected static Tranche emptyTranche(java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum> data,
                                      int minI,
                                      double ts,
                                      org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model)

getRequiredDouble

protected static double getRequiredDouble(java.util.Map<java.lang.String,java.lang.String> bindings,
                                          java.lang.String key)

getOptionalDouble

protected static double getOptionalDouble(java.util.Map<java.lang.String,java.lang.String> bindings,
                                          java.lang.String key,
                                          double defaultValue)

getRequiredInteger

protected static int getRequiredInteger(java.util.Map<java.lang.String,java.lang.String> bindings,
                                        java.lang.String key)

getOptionalInteger

protected static int getOptionalInteger(java.util.Map<java.lang.String,java.lang.String> bindings,
                                        java.lang.String key,
                                        int defaultValue)

getTruthSensitivity

protected double getTruthSensitivity()