Optimize GRanges=>RangesList


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79280 bc3139a8-67e5-0310-9ffc-ced21a209358
GIntervalTree fixes from Hector


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79281 bc3139a8-67e5-0310-9ffc-ced21a209358
Change default use.names to FALSE for readGAlignmentsList().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79796 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix bug in findOverlaps,SummarizedExperiment,Vector and
findOverlaps,Vector,SummarizedExperiment-methods. type="equal" had been
excluded.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@79797 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'

Conflicts:
	DESCRIPTION