merge GIntervalTree fix from Hector


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79824 bc3139a8-67e5-0310-9ffc-ced21a209358
Update dependency version for Rsamtools.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79853 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify unit tests to new default RleList(..., compress=TRUE); update IRanges
version dependency.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79895 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify summarizeOverlaps() examples to use 'asMates' instead 
of 'obeyQname'. Bump Rsamtools dependency version.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79975 bc3139a8-67e5-0310-9ffc-ced21a209358
Minor comment clarification in man page example.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80075 bc3139a8-67e5-0310-9ffc-ced21a209358
add GAlignmentPairs=>GAlignments coercion


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80078 bc3139a8-67e5-0310-9ffc-ced21a209358
Clean up summarizeOverlaps() and findSpliceOverlaps() 
man pages; more detail for BamFile method args.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80090 bc3139a8-67e5-0310-9ffc-ced21a209358
some changes required by recent changes to IRanges and XVector

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80126 bc3139a8-67e5-0310-9ffc-ced21a209358
more changes required by recent changes to the IRanges and XVector packages

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80271 bc3139a8-67e5-0310-9ffc-ced21a209358
- No more use of IRanges:::.bracket.Index()
- Simplify "[" method for GenomicRanges objects.
- Some tweaks to "replaceROWS" method for GenomicRanges objects.
- Replace "[" method for GAlignmentPairs objects with a "extractROWS" method.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80337 bc3139a8-67e5-0310-9ffc-ced21a209358
version bump

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80379 bc3139a8-67e5-0310-9ffc-ced21a209358
Remove unneeded "window" method for GenomicRanges objects.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80440 bc3139a8-67e5-0310-9ffc-ced21a209358
Add sortSeqlevels().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80518 bc3139a8-67e5-0310-9ffc-ced21a209358
small twek to examples

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80519 bc3139a8-67e5-0310-9ffc-ced21a209358
Make sortSeqlevels() a generic with a method for character vectors and a
default method.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80520 bc3139a8-67e5-0310-9ffc-ced21a209358
move sortSeqlevels() from R/makeSeqnameIds.R to R/seqinfo.R

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80523 bc3139a8-67e5-0310-9ffc-ced21a209358
Add tileGenome(), based on Martin's tile() proposal.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80572 bc3139a8-67e5-0310-9ffc-ced21a209358
Add 'cut.last.tile.in.chrom' arg to tileGenome().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80576 bc3139a8-67e5-0310-9ffc-ced21a209358
Add man page for tileGenome(). Rename 'tilesize' -> 'tilewidth'.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80600 bc3139a8-67e5-0310-9ffc-ced21a209358
more examples to the man page

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@80609 bc3139a8-67e5-0310-9ffc-ced21a209358