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. Cheers, H. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel