- i -

• IDENTITY : jaligner.Markups
• IGNORE_STRAND : broad.pda.seq.rap.DistanceToBED
• INCLUDE_DUPLICATES : broad.pda.samtools.PairedEndTDF
• INF : broad.core.sequence.SequenceRegion
• INNER_LENGTH : broad.pda.seq.rap.PlotAggregateRegions
• INPUT : broad.pda.samtools.FilterPairedReadsByMAQ , broad.pda.samtools.PairedEndTDF , broad.pda.samtools.TrimFastqReads , broad.pda.seq.rap.CalculateCoverageStats , broad.pda.seq.rap.CollectAnnotationEnrichments , broad.pda.seq.rap.CountProbes , broad.pda.seq.rap.ShuffleBAM , broad.pda.seq.rap.ShuffleBED , broad.pda.seq.rap.UnmarkDuplicates
• INPUT_1 : broad.pda.samtools.FilterFastqReads
• INPUT_2 : broad.pda.samtools.FilterFastqReads
• INTER_VERTICAL_SPACING : broad.core.annotation.BasicGenomicAnnotationReader
• IS_ADJACENT_AND_EMPTY : broad.core.datastructures.Interval
• IS_LEFT_OVERHANGING_OVERLAPPER : broad.core.datastructures.Interval
• IS_RIGHT_OVERHANGING_OVERLAPPER : broad.core.datastructures.Interval
• IS_STRICTLY_GREATER : broad.core.datastructures.Interval
• IS_STRICTLY_LESS : broad.core.datastructures.Interval
• IS_SUBSET : broad.core.datastructures.Interval
• IS_SUPERSET : broad.core.datastructures.Interval
• itr : umms.core.coordinatesystem.ShuffledIterator< T extends Annotation >