org.broadinstitute.hellbender.tools.walkers.vqsr

Class VQSLODTranche

java.lang.Object

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

org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche

public class VQSLODTranche
extends Tranche

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche

Tranche.TrancheComparator<T extends Tranche>, Tranche.TrancheTruthSensitivityComparator

Field Summary

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche

accessibleTruthSites, callsAtTruthSites, COMMENT_STRING, DEFAULT_TRANCHE_NAME, EXPECTED_COLUMN_COUNT, VALUE_SEPARATOR

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
int	compareTo(VQSLODTranche t)
protected static VQSLODTranche	emptyTranche(java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum> data, int minI, double trancheThreshold, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model)
java.lang.Double	getTrancheIndex()
static VQSLODTranche	mergeAndConvertTranches(java.util.List<VQSLODTranche> scatteredTranches, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode mode)
static java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.TruthSensitivityTranche>	mergeAndConvertTranches(java.util.TreeMap<java.lang.Double,java.util.List<VQSLODTranche>> scatteredTranches, java.util.List<java.lang.Double> tsLevels, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode mode)
static java.lang.String	printHeader()
static java.util.List<VQSLODTranche>	readTranches(java.io.File f) Returns a list of tranches, sorted from most to least specific, read in from file f.
java.lang.String	toString()
protected static VQSLODTranche	trancheOfVariants(java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum> data, int minI, double trancheThreshold, org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode model)

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche

getOptionalDouble, getOptionalInteger, getRequiredDouble, getRequiredInteger, getTrancheString, getTruthSensitivity, tranchesString

Methods inherited from class java.lang.Object

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

Constructor Detail

VQSLODTranche

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

Method Detail

getTrancheIndex

public java.lang.Double getTrancheIndex()

Overrides:

getTrancheIndex in class Tranche

compareTo

public int compareTo(VQSLODTranche t)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

printHeader

public static java.lang.String printHeader()

trancheOfVariants

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

emptyTranche

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

readTranches

public static java.util.List<VQSLODTranche> readTranches(java.io.File f)
                                                  throws java.io.IOException

Returns a list of tranches, sorted from most to least specific, read in from file f.

Throws:

java.io.IOException - if there are problems reading the file.

mergeAndConvertTranches

public static java.util.List<org.broadinstitute.hellbender.tools.walkers.vqsr.TruthSensitivityTranche> mergeAndConvertTranches(java.util.TreeMap<java.lang.Double,java.util.List<VQSLODTranche>> scatteredTranches,
                                                                                                                               java.util.List<java.lang.Double> tsLevels,
                                                                                                                               org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode mode)

mergeAndConvertTranches

public static VQSLODTranche mergeAndConvertTranches(java.util.List<VQSLODTranche> scatteredTranches,
                                                    org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode mode)