Document explodeCigarOps() and explodeCigarOpLengths().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77057 bc3139a8-67e5-0310-9ffc-ced21a209358
Add cigarRangesOnReference() and cigarRangesOnQuery() low-level CIGAR utilities.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77381 bc3139a8-67e5-0310-9ffc-ced21a209358
Document cigarRangesOnReference() and cigarRangesOnQuery().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77386 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix bug in cigarToIRangesListByAlignment() when 'flag' is supplied and
indicates that some reads are unmapped.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77390 bc3139a8-67e5-0310-9ffc-ced21a209358
relax SummarizedExperiment assays class validity

- dim() of length >= 2
- does not guarantee functionality; may be altered in the future


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77404 bc3139a8-67e5-0310-9ffc-ced21a209358
Use IRanges:::make_XYZxyz_to_XxYyZz_subscript() instead of .makePickupIndex().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@77409 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'