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Class
Method
Package
org
.
broadinstitute
.
gatk
.
utils
Subpackages of org.broadinstitute.gatk.utils
org.broadinstitute.gatk.utils.activeregion
org.broadinstitute.gatk.utils.analysis
org.broadinstitute.gatk.utils.baq
org.broadinstitute.gatk.utils.classloader
org.broadinstitute.gatk.utils.clipping
org.broadinstitute.gatk.utils.codecs
org.broadinstitute.gatk.utils.collections
org.broadinstitute.gatk.utils.commandline
org.broadinstitute.gatk.utils.crypt
org.broadinstitute.gatk.utils.duplicates
org.broadinstitute.gatk.utils.exceptions
org.broadinstitute.gatk.utils.fasta
org.broadinstitute.gatk.utils.file
org.broadinstitute.gatk.utils.fragments
org.broadinstitute.gatk.utils.genotyper
org.broadinstitute.gatk.utils.gga
org.broadinstitute.gatk.utils.gvcf
org.broadinstitute.gatk.utils.haplotype
org.broadinstitute.gatk.utils.haplotypebamwriter
org.broadinstitute.gatk.utils.help
org.broadinstitute.gatk.utils.instrumentation
org.broadinstitute.gatk.utils.interval
org.broadinstitute.gatk.utils.io
org.broadinstitute.gatk.utils.jna
org.broadinstitute.gatk.utils.locusiterator
org.broadinstitute.gatk.utils.nanoscheduler
org.broadinstitute.gatk.utils.pairhmm
org.broadinstitute.gatk.utils.pileup
org.broadinstitute.gatk.utils.progressmeter
org.broadinstitute.gatk.utils.r
org.broadinstitute.gatk.utils.recalibration
org.broadinstitute.gatk.utils.report
org.broadinstitute.gatk.utils.runtime
org.broadinstitute.gatk.utils.sam
org.broadinstitute.gatk.utils.smithwaterman
org.broadinstitute.gatk.utils.text
org.broadinstitute.gatk.utils.threading
org.broadinstitute.gatk.utils.variant
org.broadinstitute.gatk.utils.vectorpairhmm
org.broadinstitute.gatk.utils.wiggle
All Classes in org.broadinstitute.gatk.utils
org.broadinstitute.gatk.utils.AutoFormattingTime
org.broadinstitute.gatk.utils.AutoFormattingTimeUnitTest
org.broadinstitute.gatk.utils.BaseTest
org.broadinstitute.gatk.utils.BaseTest$TestDataProvider
org.broadinstitute.gatk.utils.BaseTest$ValidationAppender
org.broadinstitute.gatk.utils.BaseUtils
org.broadinstitute.gatk.utils.BaseUtilsUnitTest
org.broadinstitute.gatk.utils.BitSetUtils
org.broadinstitute.gatk.utils.BitSetUtilsUnitTest
org.broadinstitute.gatk.utils.ContigComparator
org.broadinstitute.gatk.utils.ContigComparatorUnitTest
org.broadinstitute.gatk.utils.DeprecatedToolChecks
org.broadinstitute.gatk.utils.ExampleToCopyUnitTest
org.broadinstitute.gatk.utils.ExampleToCopyUnitTest$MyDataProviderClass
org.broadinstitute.gatk.utils.GATKTextReporter
org.broadinstitute.gatk.utils.GenomeLoc
org.broadinstitute.gatk.utils.GenomeLocParser
org.broadinstitute.gatk.utils.GenomeLocParserBenchmark
org.broadinstitute.gatk.utils.GenomeLocParserUnitTest
org.broadinstitute.gatk.utils.GenomeLocParserUnitTest$FlankingGenomeLocTestData
org.broadinstitute.gatk.utils.GenomeLocSortedSet
org.broadinstitute.gatk.utils.GenomeLocSortedSetUnitTest
org.broadinstitute.gatk.utils.GenomeLocUnitTest
org.broadinstitute.gatk.utils.GenomeLocUnitTest$MergeTest
org.broadinstitute.gatk.utils.GenomeLocUnitTest$ReciprocalOverlapProvider
org.broadinstitute.gatk.utils.HasGenomeLocation
org.broadinstitute.gatk.utils.HeapSizeMonitor
org.broadinstitute.gatk.utils.HeapSizeMonitor$MonitorRunnable
org.broadinstitute.gatk.utils.IndelUtils
org.broadinstitute.gatk.utils.LRUCache
org.broadinstitute.gatk.utils.MD5DB
org.broadinstitute.gatk.utils.MD5DB$MD5Match
org.broadinstitute.gatk.utils.MD5Mismatch
org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary
org.broadinstitute.gatk.utils.MRUCachingSAMSequencingDictionaryUnitTest
org.broadinstitute.gatk.utils.MWUnitTest
org.broadinstitute.gatk.utils.MannWhitneyU
org.broadinstitute.gatk.utils.MannWhitneyU$DitheringComparator
org.broadinstitute.gatk.utils.MannWhitneyU$NumberedPairComparator
org.broadinstitute.gatk.utils.MathUtils
org.broadinstitute.gatk.utils.MathUtils$JacobianLogTable
org.broadinstitute.gatk.utils.MathUtils$Log10Cache
org.broadinstitute.gatk.utils.MathUtils$Log10FactorialCache
org.broadinstitute.gatk.utils.MathUtils$RunningAverage
org.broadinstitute.gatk.utils.MathUtilsUnitTest
org.broadinstitute.gatk.utils.MathUtilsUnitTest$NextCounts
org.broadinstitute.gatk.utils.MathUtilsUnitTest$PartitionGenerator
org.broadinstitute.gatk.utils.Median
org.broadinstitute.gatk.utils.MedianUnitTest
org.broadinstitute.gatk.utils.MedianUnitTest$MedianTestProvider
org.broadinstitute.gatk.utils.MendelianViolation
org.broadinstitute.gatk.utils.MultiThreadedErrorTracker
org.broadinstitute.gatk.utils.NGSPlatform
org.broadinstitute.gatk.utils.NGSPlatformUnitTest
org.broadinstitute.gatk.utils.PathUtils
org.broadinstitute.gatk.utils.PathUtils$DirectoryFilter
org.broadinstitute.gatk.utils.PathUtils$ExtensionFilter
org.broadinstitute.gatk.utils.PathUtils$OrFilenameFilter
org.broadinstitute.gatk.utils.PathUtils$isGATKVersion
org.broadinstitute.gatk.utils.PathUtilsUnitTest
org.broadinstitute.gatk.utils.QualityUtils
org.broadinstitute.gatk.utils.QualityUtilsUnitTest
org.broadinstitute.gatk.utils.RandomDNA
org.broadinstitute.gatk.utils.SampleUtils
org.broadinstitute.gatk.utils.SampleUtilsUnitTest
org.broadinstitute.gatk.utils.SequenceComplexity
org.broadinstitute.gatk.utils.SequenceDictionaryUtils
org.broadinstitute.gatk.utils.SequenceDictionaryUtils$CompareSequenceRecordsByIndex
org.broadinstitute.gatk.utils.SequenceDictionaryUtilsUnitTest
org.broadinstitute.gatk.utils.SimpleTimer
org.broadinstitute.gatk.utils.SimpleTimerUnitTest
org.broadinstitute.gatk.utils.TestNGTestTransformer
org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc
org.broadinstitute.gatk.utils.Utils
org.broadinstitute.gatk.utils.UtilsUnitTest
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