Representation and manpulation of external sequences

Memory efficient S4 classes for storing sequences "externally"
	(behind an R external pointer, or on disk).

SharedVector-class.R SharedRaw-class.R SharedInteger-class.R
SharedDouble-class.R XVector-class.R XRaw-class.R
XInteger-class.R XDouble-class.R XVectorList-class.R
XRawList-class.R XRawList-comparison.R XIntegerViews-class.R
XDoubleViews-class.R OnDiskRaw-class.R intra-range-methods.R
compact-methods.R reverse-methods.R slice-methods.R
view-summarization-methods.R updateObject-methods.R debug.R
zzz.R

Infrastructure for manipulating intervals on sequences

The package provides efficient low-level and highly reusable S4
	classes for storing ranges of integers, RLE vectors (Run-Length
	Encoding), and, more generally, data that can be organized
	sequentially (formally defined as Vector objects), as well as views
	on these Vector objects.
	Efficient list-like classes are also provided for storing big
	collections of instances of the basic classes. All classes in
	the package use consistent naming and share the same rich and
	consistent "Vector API" as much as possible.

R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.7.7)

methods, utils, stats, BiocGenerics, stats4

The following files in the 'src' directory are licensed
for all use by Jim Kent, in a manner compatible with the
Artistic 2.0 license: common.c/h, memalloc.c/h, localmem.c/h,
hash.c/h, errabort.c/h, rbTree.c/h, dlist.c/h, errCatch.h

S4-utils.R utils.R isConstant.R normarg-utils.R
subsetting-utils.R int-utils.R str-utils.R compact_bitvector.R
endoapply.R runstat.R Annotated-class.R Vector-class.R
Vector-comparison.R List-class.R AtomicList-class.R
Ranges-class.R Ranges-comparison.R IRanges-class.R
IRanges-constructor.R IRanges-utils.R DataTable-API.R
DataTable-stats.R Views-class.R Grouping-class.R
SimpleList-class.R CompressedList-class.R Rle-class.R
RleViews-class.R RleViews-utils.R AtomicList-impl.R
DataFrame-class.R DataFrame-utils.R DataFrameList-class.R
DataFrameList-utils.R RangesList-class.R GappedRanges-class.R
ViewsList-class.R RleViewsList-class.R RleViewsList-utils.R
MaskCollection-class.R RangedData-class.R FilterRules-class.R
RDApplyParams-class.R RangedData-utils.R Hits-class.R
HitsList-class.R RangesMapping-class.R IntervalTree-class.R
IntervalTree-utils.R IntervalForest-class.R
OverlapEncodings-class.R RangedSelection-class.R read.Mask.R
funprog-methods.R intra-range-methods.R inter-range-methods.R
setops-methods.R findOverlaps-methods.R nearest-methods.R
encodeOverlaps-methods.R reverse-methods.R coverage-methods.R
slice-methods.R expand-methods.R updateObject-methods.R
classNameForDisplay-methods.R test_IRanges_package.R debug.R
zzz.R