Add OnDiskRaw-class.R (not ready yet, nothing exported for now).

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76282 bc3139a8-67e5-0310-9ffc-ced21a209358
Add readXRaw() for reading raw data from an OnDiskRaw object and returning it
as an XRaw (or derived) object. Provides a cache mechanism if the full on-disk
object is requested. Based on loadSequence(). Not exported for now.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76324 bc3139a8-67e5-0310-9ffc-ced21a209358
Remove all the stuff that is now in the XVector package.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76381 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix minor issues caused by split with XVector.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76383 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix one more issue caused by split with XVector.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76386 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify select,Vector-method to prevent dropping colnames when a single
column is extracted (i.e., add drop=FALSE).


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76392 bc3139a8-67e5-0310-9ffc-ced21a209358
No check in here, just a correction to the last svn comment. The subset,Vector-method
was modified to not drop colnames, NOT the fictitious select,Vector-method.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76393 bc3139a8-67e5-0310-9ffc-ced21a209358
English: use "is split" instead of "is splitted".

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76402 bc3139a8-67e5-0310-9ffc-ced21a209358
Add a FilterMatrix class, for holding the results of multiple filters.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76418 bc3139a8-67e5-0310-9ffc-ced21a209358
export FilterMatrix constructor


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76420 bc3139a8-67e5-0310-9ffc-ced21a209358
Put the slice() generic and methods in their own file.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@76530 bc3139a8-67e5-0310-9ffc-ced21a209358
adding new IntervalTree code
Merge branch 'master' of https://github.com/hcorrada/IRanges