Add coersion method GAlignmentPairs -> GAlignmentsList.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76031 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump version.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76033 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify coercion method GAlignmentPairs -> GAlignmentsList such that
elementMetadata is not transferred.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76044 bc3139a8-67e5-0310-9ffc-ced21a209358
Change argument name from 'asProperPairs' to 'group.as.pairs' in
readGAlignmentsList().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76176 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify "show" method for Seqinfo objects to honor showHeadLines/showTailLines
global options (default is 5).


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76295 bc3139a8-67e5-0310-9ffc-ced21a209358
50x speedup or more when merging 2 Seqinfo objects, 1 very small and 1 very big

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76301 bc3139a8-67e5-0310-9ffc-ced21a209358
Add seqselect,GAlignments-method.

GAlignmentsList:
- Remove '[' and '[[' getters and setters. Use methods
  from CompressedList.

summarizeOverlaps():
- Add 'inter.feature' and 'fragments' arguments.
- Add methods for GAlignmentsList.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76306 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix bug in flank,GenomicRanges. If 'ignore.strand=TRUE' 
then 'start' was being set to TRUE.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76441 bc3139a8-67e5-0310-9ffc-ced21a209358
Need to depend on new XVector package.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76458 bc3139a8-67e5-0310-9ffc-ced21a209358
- Add unit tests for summrizeOverlaps().
- Move distance,GenomicRanges,TranscriptDb-method to GenomicFeatures.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76495 bc3139a8-67e5-0310-9ffc-ced21a209358
Oops, deleted wrong distance method. Fixed typos in man page.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76513 bc3139a8-67e5-0310-9ffc-ced21a209358
Deprecate keepSeqlevels() and renameSeqlevels() for seqlevels().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76583 bc3139a8-67e5-0310-9ffc-ced21a209358
Enhance examples for renaming seqlevels.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76602 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix behavior of count mode 'IntersectionNotEmpty' when 'inter.feature=FALSE'.
Shared regions are removed before counting.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76613 bc3139a8-67e5-0310-9ffc-ced21a209358
Moved unit tests for keepSeqlevels() and renameSeqlevels() to 
test_Seqinfo-class.R; removed test_Seqinfo-class.R.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76635 bc3139a8-67e5-0310-9ffc-ced21a209358
Add author to seqinfo man page; \seealso on deprecated seqlevels-utils 
page now points to the seqinfo page.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76665 bc3139a8-67e5-0310-9ffc-ced21a209358
Work on examples on 'seqinfo' man page and 'Seqinfo' unit tests.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76677 bc3139a8-67e5-0310-9ffc-ced21a209358
more efficient ref class constructor

- new empty instance, the update slots


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76679 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix bug in 'show' related to 'showHeaderLines' and 'showTailLines'.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76689 bc3139a8-67e5-0310-9ffc-ced21a209358
Clean up how the default value is set for 'showHeaderLines' and 'showTailLine'.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76703 bc3139a8-67e5-0310-9ffc-ced21a209358