- s -

• sample : broad.pda.seq.protection.WindowScores
• sampleModel : umms.core.model.score.MultiScore
• sampleName : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• SAVED_MODEL_STATS_EXT : broad.pda.seq.alignment.StoredAlignmentStats
• SCORE : broad.pda.seq.rap.GenomeScoringProgram , broad.pda.seq.rap.rna.TranscriptomeScoringProgram
• SEQ_ID_REC_LENGTH : broad.core.sequence.FastaQualityBinaryIO
• sequenceDirectory : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• SHORT_ENCODED_a : broad.core.sequence.Sequence
• SHORT_ENCODED_A : broad.core.sequence.Sequence
• SHORT_ENCODED_C : broad.core.sequence.Sequence
• SHORT_ENCODED_c : broad.core.sequence.Sequence
• SHORT_ENCODED_G : broad.core.sequence.Sequence
• SHORT_ENCODED_g : broad.core.sequence.Sequence
• SHORT_ENCODED_GAP : broad.core.sequence.Sequence
• SHORT_ENCODED_N : broad.core.sequence.Sequence
• SHORT_ENCODED_T : broad.core.sequence.Sequence
• SHORT_ENCODED_t : broad.core.sequence.Sequence
• SHORT_READ_FLOW : broad.core.sequence.Sequence
• shortBEDFactory : broad.core.annotation.AnnotationFactoryFactory
• signalData : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• signalName : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• signalProcessor : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• signalSamples : broad.pda.seq.protection.MultiSampleScanPeakCaller
• SIMILARITY : jaligner.Markups
• SIMPLE_ARRAY_LEFT : broad.pda.seq.rap.CountProbes
• SIMPLE_ARRAY_RIGHT : broad.pda.seq.rap.CountProbes
• SIZE : jaligner.matrix.Matrix
• sizeFile : broad.pda.seq.protection.MultiSampleScanPeakCaller
• SIZES : broad.pda.seq.rap.GenomeCommandLineProgram
• SORT_ORDER : broad.pda.samtools.FilterPairedReadsByMAQ
• source : broad.core.annotation.BasicGenomicAnnotationReader
• SPLICED : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT.EdgeSourceType
• START_CODON_PATRN : umms.core.annotation.Gene
• statistic : broad.pda.enrichment.EnrichmentMetric
• statisticName : broad.pda.enrichment.EnrichmentMetric
• STATS : broad.pda.seq.rap.CountProbes
• stepSize : broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller , broad.pda.seq.protection.WindowScores
• STOP : jaligner.Directions
• STOP_CODONS : umms.core.annotation.Gene
• SYMMETRIC : broad.pda.seq.rap.PlotAggregateRegions