Classes and Subpackages of org.broadinstitute.gatk.utils.sam

org.broadinstitute.gatk.utils.sam.AlignmentStartComparator
org.broadinstitute.gatk.utils.sam.AlignmentStartWithNoTiesComparator
org.broadinstitute.gatk.utils.sam.AlignmentUtils
org.broadinstitute.gatk.utils.sam.AlignmentUtils$CigarPairTransform
org.broadinstitute.gatk.utils.sam.AlignmentUtils$MismatchCount
org.broadinstitute.gatk.utils.sam.AlignmentUtilsUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialBAMBuilder
org.broadinstitute.gatk.utils.sam.ArtificialBAMBuilderUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialGATKSAMFileWriter
org.broadinstitute.gatk.utils.sam.ArtificialMultiSampleReadStream
org.broadinstitute.gatk.utils.sam.ArtificialPatternedSAMIterator
org.broadinstitute.gatk.utils.sam.ArtificialPatternedSAMIteratorUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialReadsTraversal
org.broadinstitute.gatk.utils.sam.ArtificialSAMFileReader
org.broadinstitute.gatk.utils.sam.ArtificialSAMFileWriterUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialSAMIterator
org.broadinstitute.gatk.utils.sam.ArtificialSAMQueryIterator
org.broadinstitute.gatk.utils.sam.ArtificialSAMQueryIteratorUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils
org.broadinstitute.gatk.utils.sam.ArtificialSAMUtilsUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream
org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamAnalyzer
org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamUnitTest
org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamUnitTest$ArtificialSingleSampleReadStreamTest
org.broadinstitute.gatk.utils.sam.BySampleSAMFileWriter
org.broadinstitute.gatk.utils.sam.CigarUtils
org.broadinstitute.gatk.utils.sam.ClippedGATKSAMRecord
org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord
org.broadinstitute.gatk.utils.sam.GATKSAMRecord
org.broadinstitute.gatk.utils.sam.GATKSAMRecordUnitTest
org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory
org.broadinstitute.gatk.utils.sam.MisencodedBaseQualityReadTransformer
org.broadinstitute.gatk.utils.sam.MisencodedBaseQualityUnitTest
org.broadinstitute.gatk.utils.sam.NWaySAMFileWriter
org.broadinstitute.gatk.utils.sam.ReadUnclippedStartWithNoTiesComparator
org.broadinstitute.gatk.utils.sam.ReadUtils
org.broadinstitute.gatk.utils.sam.ReadUtilsUnitTest
org.broadinstitute.gatk.utils.sam.ReadUtilsUnitTest$GetAdaptorFunc
org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder
org.broadinstitute.gatk.utils.sam.SimplifyingSAMFileWriter

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All Classes in org.broadinstitute.gatk.utils.sam