[Bioc-devel] new GenomicAlignments package

Hervé Pagès hpages at fhcrc.org
Mon Dec 9 22:30:24 CET 2013

Hi developpers,

Just wanted to announce the new GenomicAlignments package in BioC
devel. It's a split from the GenomicRanges package that contains:

   - The GAlignments/GAlignmentPairs/GAlignmentsList classes
     and the readGAlignment*() functions.

   - The CIGAR low-level utilities and the higher-level tools
     that make use of them (e.g. sequenceLayer(),
     stackStringsFromBam(), pileLettersAt(), etc... more will
     be added in the future).

   - summarizeOverlaps() and its vignette.

If you need any of those things in your package, you should now
'Depends' or 'Imports' GenomicAlignments in addition to
GenomicRanges (if you only use any of those things in your examples
or vignette, then please use 'Suggests' instead of 'Depends' or
'Imports'). I've tried to do this for all the software packages
in BioC devel that this split broke (based on the build/check report).
Still need to do this for some data experiment packages though
(leeBamViews, parathyroidSE, RNAseqData.HNRNPC.bam.chr14).

Please let me know if I missed your package and sorry in advance
for the inconvenience.


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