├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── AtomicList-class.R ├── AtomicList-utils.R ├── CompressedAtomicList-class.R ├── CompressedAtomicList-summarization.R ├── CompressedDataFrameList-class.R ├── CompressedGrouping-class.R ├── CompressedHitsList-class.R ├── CompressedList-class.R ├── CompressedList-comparison.R ├── CompressedRangesList-class.R ├── DataFrameList-class.R ├── DataFrameList-utils.R ├── Grouping-class.R ├── Hits-class-leftovers.R ├── IPos-class.R ├── IPosList-class.R ├── IPosRanges-class.R ├── IPosRanges-comparison.R ├── IRanges-class.R ├── IRanges-constructor.R ├── IRanges-utils.R ├── IRangesList-class.R ├── IntegerRangesList-class.R ├── MaskCollection-class.R ├── NCList-class.R ├── RangedSelection-class.R ├── Ranges-and-RangesList-classes.R ├── Rle-class-leftovers.R ├── RleViews-class.R ├── RleViews-summarization.R ├── RleViewsList-class.R ├── RleViewsList-utils.R ├── SimpleGrouping-class.R ├── Vector-class-leftovers.R ├── Views-class.R ├── ViewsList-class.R ├── cbind-Rle-methods.R ├── coverage-methods.R ├── cvg-methods.R ├── extractList.R ├── extractListFragments.R ├── findOverlaps-methods.R ├── inter-range-methods.R ├── intra-range-methods.R ├── makeIRangesFromDataFrame.R ├── multisplit.R ├── nearest-methods.R ├── range-squeezers.R ├── read.Mask.R ├── reverse-methods.R ├── seqapply.R ├── setops-methods.R ├── slice-methods.R ├── subsetting-utils.R ├── thread-control.R ├── tile-methods.R ├── windows-methods.R └── zzz.R ├── README.md ├── TODO ├── inst ├── CITATION ├── extdata │ ├── ce2chrM.bed │ ├── ce2chrM.fa.out │ ├── hg18liftAll.lft │ └── hs_b36v3_chrY.agp ├── include │ ├── IRanges_defines.h │ ├── IRanges_interface.h │ └── _IRanges_stubs.c └── unitTests │ ├── test_AtomicList-class.R │ ├── test_AtomicList-summarization.R │ ├── test_AtomicList-utils.R │ ├── test_DataFrame-utils.R │ ├── test_DataFrameList.R │ ├── test_Grouping-class.R │ ├── test_HitsList.R │ ├── test_IPos-class.R │ ├── test_IRanges-class.R │ ├── test_IRanges-constructor.R │ ├── test_IRangesList-class.R │ ├── test_NCList-class.R │ ├── test_Ranges-comparison.R │ ├── test_RleViews.R │ ├── test_RleViewsList.R │ ├── test_coverage-methods.R │ ├── test_extractList.R │ ├── test_findOverlaps-methods.R │ ├── test_inter-range-methods.R │ ├── test_intra-range-methods.R │ ├── test_makeIRangesFromDataFrame.R │ ├── test_nearest-methods.R │ ├── test_seqapply.R │ ├── test_setops-methods.R │ ├── test_split.R │ ├── test_splitListElements.R │ └── test_tile-methods.R ├── man ├── AtomicList-class.Rd ├── AtomicList-summarization.Rd ├── AtomicList-utils.Rd ├── CompressedHitsList-class.Rd ├── CompressedList-class.Rd ├── DataFrameList-class.Rd ├── Grouping-class.Rd ├── Hits-class-leftovers.Rd ├── IPos-class.Rd ├── IPosRanges-class.Rd ├── IPosRanges-comparison.Rd ├── IRanges-class.Rd ├── IRanges-constructor.Rd ├── IRanges-internals.Rd ├── IRanges-utils.Rd ├── IRangesList-class.Rd ├── IntegerRanges-class.Rd ├── IntegerRangesList-class.Rd ├── MaskCollection-class.Rd ├── NCList-class.Rd ├── RangedSelection-class.Rd ├── Rle-class-leftovers.Rd ├── RleViews-class.Rd ├── RleViewsList-class.Rd ├── Vector-class-leftovers.Rd ├── Views-class.Rd ├── ViewsList-class.Rd ├── coverage-methods.Rd ├── extractList.Rd ├── extractListFragments.Rd ├── findOverlaps-methods.Rd ├── inter-range-methods.Rd ├── intra-range-methods.Rd ├── makeIRangesFromDataFrame.Rd ├── multisplit.Rd ├── nearest-methods.Rd ├── range-squeezers.Rd ├── read.Mask.Rd ├── reverse-methods.Rd ├── seqapply.Rd ├── setops-methods.Rd ├── slice-methods.Rd └── view-summarization-methods.Rd ├── src ├── CompressedAtomicList_utils.c ├── CompressedIRangesList_class.c ├── CompressedList_class.c ├── Grouping_class.c ├── IPosRanges_comparison.c ├── IRanges.h ├── IRanges_class.c ├── IRanges_constructor.c ├── Makevars ├── NCList.c ├── R_init_IRanges.c ├── Ranges_class.c ├── RleViews_summarization.c ├── S4Vectors_stubs.c ├── SimpleIRangesList_class.c ├── coverage_methods.c ├── extractListFragments.c ├── inter_range_methods.c └── 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