March 10, 2014
Viewdc71e3a

Port change from devel that prevents conflict between cached TP53 genomes

Michael Lawrence authored on 10/03/2014 23:32:24
July 15, 2013
Viewf3db568

renamed summarizeVariants to variantSummary the which in GsnapParam is now a GenomicRanges instead of a RangesList refactor the show method of BamTallyParam to rely on showAsCell

Michael Lawrence authored on 15/07/2013 23:41:54
July 14, 2013
View59c3684

Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

Michael Lawrence authored on 14/07/2013 00:43:43
May 13, 2013
View0dbb11f

Use readDNAStringSet() instead of read.DNAStringSet().

Herve Pages authored on 13/05/2013 23:23:36
March 30, 2013
View82c0838

import 'exons'

Michael Lawrence authored on 30/03/2013 02:36:06
March 27, 2013
View2f697ca

Add GmapGenome->DNAStringSet coercion, exports the whole genome sequence. This means export(x, "genome.fasta") should work.

Michael Lawrence authored on 27/03/2013 19:11:09
March 26, 2013
View248ed95

Export new stuff, bump version

Michael Lawrence authored on 26/03/2013 21:44:37
September 29, 2012
View7afec90

drop import of parallel package, as we apparently do not use it?

Michael Lawrence authored on 29/09/2012 04:03:09
September 12, 2012
View3dd29e4

Export TP53Which()

Michael Lawrence authored on 12/09/2012 05:15:05
September 11, 2012
View297de88

*gmapR option name for returning system calls is now "systemCallMode"

Cory Barr authored on 11/09/2012 22:12:30
View1116df9

added capability to overwrite .system via providing a function to options('gmapRSysCall')

Cory Barr authored on 11/09/2012 02:32:47
September 10, 2012
View9dfa7ad

added patches supplied by Greg

Cory Barr authored on 10/09/2012 22:52:34
September 7, 2012
View1e5e275

Fix typo in spliceSites<-

Michael Lawrence authored on 07/09/2012 17:05:26
Viewe35b784

Fix import of getSeq

Michael Lawrence authored on 07/09/2012 17:02:06
View5fdf642

Add a GRangesList spliceSites<- method. Seems like it is working, but more testing is needed.

Michael Lawrence authored on 07/09/2012 16:50:04