Do not force global options 'showHeadLines' and 'showTailLines' to numeric in
.compactDataFrame (allow 'Inf' value).


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77586 bc3139a8-67e5-0310-9ffc-ced21a209358
Add low-level CIGAR utility cigarRangesOnPairwiseSpace().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77612 bc3139a8-67e5-0310-9ffc-ced21a209358
Make 'showHeadLines' and 'showTailLines' robust to NA, Inf and numeric.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77633 bc3139a8-67e5-0310-9ffc-ced21a209358
- Rename cigarToWidth() -> cigarWidthOnReferenceSpace(), and cigarToQWidth() ->
  cigarWidthOnQuerySpace(). Make the old names aliases for the new names and
  deprecate them.
- Add cigarWidthOnPairwiseSpace().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77643 bc3139a8-67e5-0310-9ffc-ced21a209358
Deprecate cigarToIRanges().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77645 bc3139a8-67e5-0310-9ffc-ced21a209358
Some code simplifications.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77652 bc3139a8-67e5-0310-9ffc-ced21a209358
- Add 'f' argument to cigarRangesOnReferenceSpace().
- More code simplifications.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77654 bc3139a8-67e5-0310-9ffc-ced21a209358
- Add 'remove.N.regions' argument to cigarRangesOnReferenceSpace(),
  cigarRangesOnPairwiseSpace(), cigarWidthOnReferenceSpace(), and
  cigarWidthOnPairwiseSpace().
- Add 'before.hard.clipping' and 'after.soft.clipping' arguments to
  cigarRangesOnQuerySpace().
- Add 'after.soft.clipping' argument to cigarWidthOnQuerySpace().
- Add 'flag' argument to cigarWidthOnReferenceSpace(), cigarWidthOnQuerySpace(),
  and cigarWidthOnPairwiseSpace().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77679 bc3139a8-67e5-0310-9ffc-ced21a209358
Add extractAlignmentRangesOnReference() as a replacement for now deprecated
cigarToIRangesListByAlignment() and cigarToIRangesListByRName().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77682 bc3139a8-67e5-0310-9ffc-ced21a209358
Rename 'remove.N.regions' arg -> 'N.regions.removed'.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77686 bc3139a8-67e5-0310-9ffc-ced21a209358
- Deprecate splitCigar().
- Add 'ops' argument to explodeCigarOps() and explodeCigarOpLengths().


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77708 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix regression introduced in previous commit in cigarOpTable().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77709 bc3139a8-67e5-0310-9ffc-ced21a209358
Resolve ambiguities in method dispatch:
- Add countOverlaps methods for GRangesList,GAlignments (and vice versa),
  GenomicRanges,GAlignments (and vice versa), and GAlignmentPairs,GAlignmentPairs.
- Add findOverlaps methods for GRangesList,GAlignments (and vice versa).



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77762 bc3139a8-67e5-0310-9ffc-ced21a209358
Use get_showHeadLines() and get_showTailLines() helpers 
in Seqinfo and GRanges show methods.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77781 bc3139a8-67e5-0310-9ffc-ced21a209358
Remove ':::' since show*Lines helpers are now exported from IRanges.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77783 bc3139a8-67e5-0310-9ffc-ced21a209358
Add seqlevelsInUse() getter for GRanges, GRangesList, GAlignments,
GAlignmentPairs, GAlignmentsList, and SummarizedExperiment objects.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77947 bc3139a8-67e5-0310-9ffc-ced21a209358
Minor tweak to how "findOverlaps" method for GRanges objects handles circular
sequences.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77999 bc3139a8-67e5-0310-9ffc-ced21a209358
Thanks to Herve for these performance improvements to summarizeOverlaps():
- Union(): 1.5x to 2x speedup.
- IntersectionStrict(): Code clean up + bug fix for reads on 
  circular sequence.
- IntersectionNotEmpty(): 2x to 8x speedup + memory footprint 
  reduced by ~half. Bug fix for missed hits when 'features' has 
  '-' and '+' strand elements and ignore.strand=TRUE.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78046 bc3139a8-67e5-0310-9ffc-ced21a209358
Add code comment.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78047 bc3139a8-67e5-0310-9ffc-ced21a209358
Small code simplification in .removeSharedRegions() internal helper.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78055 bc3139a8-67e5-0310-9ffc-ced21a209358