fix unlisting of lists of VRanges; add showAsCell,GenomicRanges


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78476 bc3139a8-67e5-0310-9ffc-ced21a209358
add GIntervalTree by Hector Corrada Bravo


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78477 bc3139a8-67e5-0310-9ffc-ced21a209358
fix conversion of extra column slots to data.frame


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78573 bc3139a8-67e5-0310-9ffc-ced21a209358
updates for GIntervalTree


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78583 bc3139a8-67e5-0310-9ffc-ced21a209358
Add 'dense' argument to cigarRangesOnPairwiseSpace() and cigarWidthOnPairwiseSpace().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78625 bc3139a8-67e5-0310-9ffc-ced21a209358
Rename cigarRangesOn*Space() functions -> cigarRangesAlong*Space() and
cigarWidthOn*Space() functions -> cigarWidthAlong*Space().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78627 bc3139a8-67e5-0310-9ffc-ced21a209358
minor edit

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78648 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'

Conflicts:
	DESCRIPTION
	R/GIntervalTree-class.R
Fixes to GIntervalTree

* Problems with empty seqlevels and out-of-order seqinfo are fixed in version 1.19.20 of IRanges
* Unit tests to check these cases added here
* Removed show,GIntervalTree-method to use the inherited GenomicRanges method
minor edit
bump IRanges version dependency